Harbaugh questioned two non-calls in the final series when the 49ers failed to convert with a first and goal as they looked to find receiver Michael Crabtree with the game on the line.
"There's no question in my mind that there was a pass interference and then a hold on Crabtree on the last one," said Harbaugh.
The 49ers coach was also unhappy with, on Baltimore's subsequent possession, the failure of officials to call holding as Ravens punter Sam Koch took a safety to eat up time.
"I still haven't gotten an explanation on the safety. It was obviously the intent of the Ravens to tackle and hold... but not one holding flag came out," he said.
"I realize I am on the side of the 49ers, I'm the coach and probably have some bias there but in my mind I thought it was obvious, but that's not the way they saw it," he added.
Harbaugh also protested the decision to penalize his cornerback Chris Culliver for pass interference, allowing the Ravens to make a crucial first down after Joe Flacco had thrown an incomplete pass on third down with the score 31-29.
"I didn't think that was an interference," said Harbaugh.
But the 49ers coach was also critical of his players, who paid the price for turnovers and penalties.
"We want to handle this with class and grace. We had several opportunities in the game. We didn't play our best game. Ravens made a lot of plays. Our guys battled back to get in it. We competed and battled to win," he said.
Asked about his failure to give running back Frank Gore a chance to burst into the end-zone on the three failed attempts to score from five yards out, Harbaugh simply said: "We had other plays called."
