SANTA CLARA, Calif. — Before he starts counting how many receivers the Denver Broncos have on the field Sunday night, San Francisco 49ers coach Jim Harbaugh would like to know how many healthy defensive backs he has to cover them.

If the matchup occurred Wednesday, Harbaugh would have been at a distinct numerical disadvantage.

Less than 48 hours after recording a road win at St. Louis on Monday night, the 49ers began preparations for their showdown with the Broncos with nickel corner Jimmie Ward sidelined Wednesday with a quad injury.

What Ward watched at practice was a bunch of his mates limping around at far less than game speed.

–Cornerback Tramaine Brock, out since Week 3 with a turf-toe injury, returned to practice, but only in a limited capacity.

–Cornerback Perrish Cox, who has been borderline brilliant in Brock’s place, also was limited with a quad injury.

–Cornerback Chris Culliver, who started all six games across from Brock and Cox, avoided contact during the workout because of a shoulder injury.

–Cornerback Chris Cook, who was on the field for 19 snaps Monday because of Ward’s injury, also suffered Wednesday from the quad epidemic.

Among the five guys who shared time at the cornerback positions Monday, only rookie Dontae Johnson was a full participant at practice Wednesday.

Is it a concern? Of course.

Is it an even bigger concern being that these are the guys who are expected to be chasing around the Broncos’ Demaryius Thomas, Wes Welker and Emmanuel Sanders on Sunday night? Well, duh.

“We’re excited to compete,” Harbaugh said Wednesday, trying to put a positive spin on the matchup. “It starts today — competition, understanding our opponent and preparing for them.”

The team arguably was in worse shape at linebacker.

Already without suspended Aldon Smith and injured NaVorro Bowman, the 49ers learned Wednesday that Patrick Willis is unlikely to play against the Broncos because of a toe injury suffered in Monday’s win over the St. Louis Rams.

Harbaugh said the club got good news when an examination of Willis’ injury disclosed it’s not turf toe. “I don’t think it’s a long-term thing,” he reported.

Harbaugh added Willis would be examined on a daily basis, and that the toe injury is not considered to be as serious as the one suffered by cornerback Tramaine Brock in Week 2. Brock has missed the last four games.

Chris Borland, who replaced Willis for his first 31 defensive snaps of the season Monday, will work out with the first team this week.

“He’s shown that he can play,” Harbaugh said. “This past week, tackled well, broke up two passes. Excited for him.”

Worth noting, Sunday’s matchup between the 49ers and Broncos will be the first since Peyton Manning left the Indianapolis Colts for Colorado.

For a time, San Francisco was discussed as his destination. That was never a serious possibility, Manning explained Wednesday.

Asked if the 49ers had “pursued” him following the 2011 season or if they were merely “evaluating” him, Manning responded, “I don’t know what the verb is or if it really matters.”

“I enjoyed the time that I spent with the 49ers personnel, with the coach, general manager,” he continued. “They’re a first-class organization and there’s a reason why they’re so successful.”

Harbaugh said he hoped Manning’s response would put to rest rumors of the 49ers “pursuing” the future Hall of Famer when they already had an established quarterback in Alex Smith.

“I keep hearing it over and over,” he said. “It’s silly and it’s untrue. It’s phony. Even the perception that we were pursuing. We were evaluating.”

NOTES: Uncovering no proof that 49ers QB Colin Kaepernick used a racial slur in a verbal altercation with Chicago Bears DE Lamarr Houston in Week 2, the NFL agreed to trim a $11,025 fine in half. Kaepernick appealed the fine he received after the Sept. 14 incident, which also drew an unsportsmanlike-conduct penalty. The NFL said while it found no proof of a racial slur, it did determine that Kaepernick used “general profane language” when taunted by Houston after an interception. Because of that, the league determined a small fine was warranted. … Among those practicing on a limited basis Wednesday were WR Steve Johnson (hip), OT Anthony Davis (knee) and NT Ian Williams (ankle).