Ravens rush linebacker Terrell Suggs was penalized for unnecessary roughness in the final minute when he tackled quarterback EJ Manuel and knocked his helmet off.
Manuel was in the process of kneeling down to try to run out the clock, but he didn't immediately go to the ground as Suggs defended the play, unsuccessfully trying to force a fumble to get the ball back.
When asked if referee Jerome Boger explained the thinking behind the call, Harbaugh replied: "Not a very good one."
Harbaugh defended Suggs' actions.
"I think the quarterback is responsible for taking a knee there," Harbaugh said. "He's got to get his knee down. He should do it more quickly and not burn more time off the clock. That is something we hear from the league all the time.
"His knee was not on the ground. I'm just disappointed that Terrell wasn't able to cause a fumble there. He definitely did the right thing in that situation."
In the locker room following the game, Suggs said that Boger told him that he had safety in mind when he called the penalty.
"Jerome Boger actually said he's got to err on the side of safety," said Suggs, who recorded a game-high 17 tackles, one sack and three quarterback hits in a losing cause. "He said, 'The thing was that his helmet came off.' Anytime a quarterback's helmet comes off, he's got to look at it. I can't whine about it."