The Niners could only muster two David Akers field goals in the first-half as Joe Flacco threw three touchdowns to Anquan Boldin, Dennis Pitta and Jacoby Jones.
Jones then scored a record-equaling 108-yard kick return as the second-half began, but after a power outage delay, San Francisco’s offence finally kicked into gear.
First Colin Kaepernick found Michael Crabtree in the end zone and then handed off to Frank Gore for a touchdown to bring the 49ers back in the game.
Field goals were then exchanged, but as the 49ers chased a remarkable comeback win, Harbaugh believed officials failed to award his side a certain penalty as they lost 34-31.
Harbaugh felt there was a clear pass-interference on the 49ers final play which
cost his side a potential winning score, and did not hold back when criticising the decisions.
“There’s no question in my mind that there was a pass-interference and then a hold on Crabtree on the last one,” he said.
“Again, I realise I’m on the side of the 49ers, I’m the coach of the 49ers. I probably have some bias there.”
To see out the game, the Ravens offence deliberately conceded a safety – something that incensed the Niners coach and left him wanting an explanation.
“It was obviously the intent of the Ravens to tackle and hold, but not one holding flag came out,” he explained.
“It’s a good scheme on their part and you teach them just to tackle when you’re taking a safety like that, but not one holding penalty was called.
“I haven’t been given an explanation.”
But the first San Francisco head coach to oversee a Super Bowl defeat praised the effort of his players after they battled their way back in to the game.
“The Ravens made a lot of plays, but our guys battled back to get back in it. We competed and battled to win,” he added.
“We want to handle this with class and grace. We had several opportunities in the game, but we didn’t play our best game.”