SANTA CLARA, Calif. — Jim Harbaugh finally won his Super Bowl on Sunday.

The trophy: A game-used football.

For the first time in his four seasons with the 49ers, Harbaugh’s season ended with a victory when San Francisco beat the playoff-bound Arizona Cardinals 20-17 in the regular-season finale.

After losing twice in the NFC Championship Game and once in the Super Bowl in the past three seasons, the 49ers’ goal this year was to win their final game.

That they did.

But he won’t be going to Disneyland. He is headed to Michigan to coach the Wolverines after a decision described as a “mutual” parting with the 49ers.

“It felt great to win,” Harbaugh insisted shortly after getting a Gatorade shower from his players. “I count them up. I count up these wins and that’s 49 wins and that seems appropriate. That seems pretty darn good.”

To no one’s surprise, the 49ers announced after the game that the organization and Harbaugh had agreed to part ways.

After an 8-8 record in 2014, Harbaugh’s four-year record: 49 wins, 19 losses, one tie and no Lombardi Trophies.

This was the year when making room in the trophy case for a sixth Lombardi seemed to make the most sense.

The 49ers were a tipped pass away from beating the eventual champion Seattle Seahawks in the NFC title game a year ago, they had addressed their few weakness with a strong draft, and perhaps most important, they were expecting Colin Kaepernick, paid handsomely to be a franchise quarterback, to take that next step to stardom under Harbaugh and lead the 49ers to new heights.

Alas, things went south in a hurry. Friction between Harbaugh and management was being reported even before the first snap of the season.

Kaepernick showed signs of things to come with three costly interceptions in a 28-20 loss to the Chicago Bears in the grand opening of $1.3 billion Levi’s Stadium in Week 2. And at midseason, the club’s three best players — linebackers Aldon Smith, NaVorro Bowman and Patrick Willis — weren’t playing because of a suspension (Smith missed the first nine games), an injury suffered last season (Bowman sat out all of 2014) and an injury suffered in Week 7 (Willis missed the last 10 games).

A rock-bottom loss at rival Oakland in Week 14, sandwiching a crushing sweep at the hands of the Seahawks, sealed the deal, setting up Harbaugh to accept a deal he couldn’t resist or refuse from the University of Michigan.

The 49ers had to band together one final time to get their coach a going-away gift.

“It meant a lot. Much appreciated,” Harbaugh gushed afterward. “Just the way I feel about these players, these coaches, this staff, this organization. Been the time of my life. Been a lot of great memories, great moments.

“We accomplished great things. Tremendous football. So many people to thank for that. Feel great to be a part of it. Feel it’s been signature years in my life and I have much gratitude for everyone involved.”

–Harbaugh did not address the media at the 49ers’ practice facility Monday, so it was left to team CEO Jed York and general manager Trent Baalke to explain the “mutual” aspect of the team’s announcement it was parting ways with its coach Sunday.

“It wasn’t an easy conclusion to get to,” York said of a series of discussions he’d had with Harbaugh in the aftermath of not being able to agree upon a contract extension last off-season.

“Ultimately,” he continued, “we came to the conclusion that it was best for us to go in different directions.”

Several reports over the course of the 49ers’ disappointing 8-8 season described a power struggle between Harbaugh and Baalke. The GM downplayed such a thing Monday, saying the decision to go with a new coach was partly a product of the bad season and partly a product of philosophical differences.

“We don’t raise division championship banners; we don’t raise NFC championship banners,” Baalke said of the franchise’s high expectations. “We raise Super Bowl banners.

“We look forward to getting this thing back on track and getting (the fans) exactly what (they) deserve.”

Speaking directly about Harbaugh, Baalke insisted, “We’ve had philosophical discussions. And when we sat down, we just couldn’t come to a place where we thought moving together was the best for either party. It wasn’t us saying, ‘Jim, you’re fired.’ This wasn’t Jim saying, ‘I don’t want to be here.’

“It was a discussion that took place over a decent amount of time to figure out what’s best for everybody involved, and it was the conclusion that we came to.”

Notes: Running back Frank Gore rushed for 144 yards in Sunday’s win. That is 31 yards more than any other back gained against the Cardinals this season. Gore finished the season ranked ninth in the NFL in rushing with 1,106 yards, his fourth consecutive 1,000-yard season and eighth in his 10-year career. Only 11 players in NFL history have run for 1,000 or more yards eight times. Gore rushed for more than 100 yards in four games this season — all quality opponents: Philadelphia, Kansas City, San Diego and Arizona. The 49ers went 3-1 in those games, losing only to the Chargers in overtime.

REPORT CARD VS. CHARGERS

–PASSING OFFENSE: B-plus — Against a good defense, Colin Kaepernick had the type of game that was supposed to separate him from most quarterbacks this season. He was effective both throwing (204 yards, two touchdowns, no interceptions) and scrambling when he needed to avoid sacks (seven runs, 63 yards). The only thing missing from the 49ers’ passing game was tight end Vernon Davis, who caught the only ball thrown his way for a nine-yard gain.

–RUSHING OFFENSE: A-plus — Frank Gore finished the season with a flourish. In what might have been his best effort of the season, he put up 144 yards against a truly elite run defense. The 144 yards were 31 more than any other back amassed against the Cardinals this season. As a team, the 49ers went over 200 yards against a unit that had held its first 15 opponents to an average of less than 100 yards.

–PASSING DEFENSE: B-minus — The 49ers gave up 316 yards and two touchdowns to a guy who was so bad in his previous effort, he was benched in favor of a fourth-stringer who demonstrated in practice he wasn’t worthy of a promotion in the first place. That said, they did harass Ryan Lindley into three interceptions and limited Larry Fitzgerald to two catches.

–RUSHING DEFENSE: B-plus — The Cardinals didn’t expect to run the ball on the 49ers’ stellar run defense, and basically they didn’t. They were held under 100 yards despite trying 25 times. Their per-carry average was just 3.9 yards. And they never broke off a run longer than 11 yards. It wasn’t a complete shut-down, but enough to force the Cardinals into a passing mode most of the afternoon.

–SPECIAL TEAMS: A — The 49ers got the better of the Cardinals in every aspect of special teams — returns, punts and field goals. In a close game where one mistake in the kicking game could have spelled the difference between a win and a loss, the 49ers performed flawlessly.

–COACHING: A — Sunday’s NFL schedule pitted eight teams either already going to the playoffs or trying to clinch a spot against clubs playing out the string. The team with the incentive won six of those games by an average of 17.8 points. Only the Bills (against New England) and the 49ers demonstrated even an ounce of pride. In the 49ers’ case, the coach provided all the motivation.