There was the pass-interference penalty by nickel back Chris Culliver for 14 yards, and an encroachment penalty on the same drive that led to a 38-yard field goal by the Ravens' Justin Tucker with 4:19 remaining.
"There were some big penalties," Jim Harbaugh said. "The 5-yard variety really hurt us in the game."
The brothers each had their share of bold decisions in Super Bowl XLVII.
When the 49ers scored a touchdown to cut the Ravens' lead to 31-29 with 9:57 left in the fourth, Jim Harbaugh decided to go for two. But John Harbaugh countered with an all-out blitz that forced a throwaway by Kaepernick.
Jim Harbaugh later wisely but boldly challenged a spot, won the challenge and took away a first down from the Ravens with under eight minutes remaining.
John Harbaugh got a little cute late in the second quarter. Instead of going for a 31-yard field goal, Harbaugh, the former special teams coach, called for the first fake field goal in Super Bowl history.
Tucker took the direct snap and ran left, but on fourth-and-9, Tucker was stopped eight 8 yards by Darcel McBath.
The energy that was drained from the Superdome shortly after halftime seemed to be pumped into the 49ers by their coach. After the power outage, the 49ers took advantage of every opportunity the Ravens presented to score 24 of the next 27 points.
"There is no greater competitor," John said. "There is no greater coach in the National Football League or in the world as far as I'm concerned, than Jim Harbaugh. The way that team played proves it.
"What they have done the last two years is unprecedented. They showed it today the way they battled back and fought right to the end. That is who he is and that is who they are. I could not be more proud of him and what he has done."
But a sharp move by John in the final seconds helped preserve the victory. He decided to have punter Sam Koch take a safety and run eight seconds off the clock so the 49ers would get the ball back with four seconds left down three.
John Harbaugh and Jim Harbaugh always brought out the best in each other through competition — hard, beautiful competition.
They did it again Sunday.