SANTA CLARA, Calif. — Labeling it “not insubordination,” San Francisco 49ers coach Jim Harbaugh welcomed veteran outside linebacker Ahmad Brooks back to practice Wednesday after he had had a run-in with defensive assistant Jim Tomsula during Sunday’s win over the New York Giants.

Brooks disclosed Wednesday he had been benched for the remainder of Sunday’s game after getting into a shouting match with Tomsula on the sideline late in the first quarter.

Initially, it had been speculated that Brooks took himself out of the game, but he insisted Wednesday that was not the case.

“I did not quit on the team. I did not take myself out of the game,” he insisted. “But words that were said by me obviously could not be taken back, so they decided to not put me back in the game.”

Brooks reportedly was upset to learn that he would be sharing time with impressive rookie Aaron Lynch in the New York game. Both had started the game, but one spot became unavailable to them once fellow outside linebacker Aldon Smith took the field for the first time on the Giants’ third possession.

Harbaugh would not say who will start Sunday against the Washington Redskins, but assured Brooks would be in the mix.

“I believe in Ahmad Brooks. (I) know he’s going to make a vital contribution to our team, as he always has,” Harbaugh said. “The cold, hard facts are: The last 58 games, he’s started the last 58 games. So nobody has answered the bell more than Ahmad Brooks has for this football team.”

Brooks said he apologized to his teammates and coaches.