Officials determined that cornerback Jimmy Smith's contact with Crabtree was incidental, but Harbaugh insisted a penalty should have been called.
"I really want to handle this with class and grace, and we had several opportunities in this game," said Harbaugh, who also claimed that Baltimore committed a pass interference penalty against Crabtree on second-and-goal. "We didn't play our best game, and the Ravens made a lot of plays and battled back.
"They competed to win. But there's no question in my mind that there was a pass interference -- and then a hold on Crabtree on the last one."
Harbaugh later stopped in the middle of his postgame news conference to reiterate his dissatisfaction with the officiating on the fourth-and-goal play.
"I realize I'm on the side of the 49ers," he said. "I'm the coach of the 49ers -- there is some bias there. But I wouldn't be bringing it up unless it was obvious. But that's not the way (the refs) saw it. That's the only reason I bring it up."
Crabtree, who finished with five catches for 109 yards and a touchdown, apparently agreed with Harbaugh's assessment of the play.
"When somebody grabs you, you always expect a call," Crabtree told the San Jose Mercury News. "But you can't whine to the refs. It is what it is."
Mike Pereira, the former NFL vice president of officiating, agreed with the officials' decision to not throw a flag on the play.
"Tough play that is really close both ways. Good job not calling anything," Pereira tweeted.
Crabtree also told the Mercury News that he believed he was interfered with on multiple plays in San Francisco's 34-31 loss.
"There was a couple of plays where the guy was on me before the ball got to me," he told the paper. "I don't even want to talk about it. It's frustrating, man. It's the game-winning touchdown -- makes me sad. It's the Super Bowl. It's what you live for."