Colin Kaepernick #7 of the San Francisco 49ers throws a...

Colin Kaepernick #7 of the San Francisco 49ers throws a pass during the Super Bowl against the Baltimore Ravens. (Feb. 3, 2013) Credit: Getty

NEW ORLEANS -- Fourth-and-goal from the 5-yard line. The San Francisco 49ers seemed destined to pull out another Super Bowl win, and young quarterback Colin Kaepernick was going to be the hero.

He targeted Michael Crabtree, who appeared to be held by Jimmy Smith as he chased the pass in the end zone. The ball fell incomplete, much to the irritation of 49ers coach Jim Harbaugh, who saw a penalty that wasn't called.

"I want to handle this with as much class and grace as I can," Harbaugh said after the Baltimore Ravens hung on for a 34-31 win in Super Bowl XLVII. "We had several opportunities in this game. But there was no question in my mind there was a pass interference, a hold on Crabtree on the last one."

After the play, Harbaugh, in his familiar black sweatshirt and khaki pants, pulled the cap on his head and chased after the official. The anger showed in his face, but the call stood. It was just another incomplete pass.

With 1:46 remaining, the ball was turned over to the Ravens on downs, and punter Sam Koch took an intentional safety with four seconds remaining as Baltimore held on.

The 49ers lost for the first time in six Super Bowl appearances. Jim Harbaugh also lost to brother John, who is 2-0 against him. John's Ravens beat the 49ers last season when the teams met on Thanksgiving.

Jim Harbaugh conceded the 49ers committed too many key penalties in the opening quarter. Vernon Davis caught a 20-yard pass from Kaepernick on the first play from scrimmage, only to have it called back because of an illegal-formation call on Davis. There also were a couple of offside calls that kept Ravens drives alive.

But Harbaugh's focus was on the Crabtree play. He insisted the receiver was prevented from grabbing the pass, which would have given the 49ers the lead with 1:46 remaining. He also was displeased about a non-call two plays earlier.

"I have some bias," Harbaugh said, "but that's the way I saw those plays."

The 49ers had climbed all the way back from a huge hole. Down 28-6 early in the third quarter, they pulled within 31-29 at one point and trailed 34-29 when the Ravens made their goal-line stand.

Kaepernick, in only his 10th start since replacing Alex Smith in November, seemed uncomfortable at first, throwing his passes too hard, including an interception in the second quarter.

Kaepernick rebounded nicely, however, and led the comeback. He finished 16-for-28 passing for 302 yards to join Joe Montana and Steve Young as 49ers quarterbacks who have passed for at least 300 yards in a Super Bowl.

Harbaugh was questioned about the play-calling in the 49ers' last sequence. San Francisco had first-and-goal from the 7, but after a 2-yard run, the team threw three straight times to Crabtree, all incomplete.

"Second down was an option," Harbaugh said, "and Colin passed. We were right on the brink of winning it. It was a heck of a football game."