INDIANAPOLIS – Flawless. That was the word the 49ers preached all week as they prepared for the undefeated Colts. They would have to play mistake-free football to hand Peyton Manning, Reggie Wayne and Dwight Freeney their first loss of the season.

They didn't.

As was the case earlier this season in Minneapolis, the 49ers were tougher and hungrier and leading late in the second half. But in falling 18-14 Sunday, they continue to be the gutsy young track runner who comes close to winning the race but can't quite make it over that final hurdle. That kid gets a nice, warm ovation at the end of the race. But he walks away with a skinned knee instead of a shiny trophy.

The 49ers are definitely bleeding.

In addition to losing their third consecutive game and falling under .500 for the first time this season, starting left tackle Joe Staley was lost for the game on the first offensive play and Nate Clements, who entered the season billed as the 49ers' top cornerback, could be lost for the season. Staley sprained a knee when someone rolled onto the back of his leg, and Clements broke his shoulder blade. Both will be re-evaluated today.

For Clements, it was a case of adding injury to insult.

Despite being healthy to start the game, the $80 million cornerback was on the sideline while Tarell Brown started in his place. After the game, coach Mike Singletary said the thinking was that Brown and Shawntae Spencer matched up better against the Colts' wide receivers than Clements.

Clements played a handful of defensive snaps before the injury, but his role mostly was as the team's punt returner. He absorbed and delivered several big hits while returning punts, but it wasn't immediately clear if that's what caused his injury. The 49ers will have to decide whether to place Clements on injured reserve, a move that would end his season.

That the Colts had to dust off a trick play to win the game shows just how close the 49ers came to pulling off one of the biggest upsets of the season. While Manning engineered a game-winning drive in the fourth quarter or overtime for the 38th time in his career, he was held without a touchdown pass.

Instead, it was tailback Joseph Addai who tossed the 22-yard winning score to a diving Wayne in the back of the end zone. The defensive back who was victimized on the play was Spencer, who to that point played just about as well as any cornerback does against the Colts.

Spencer said the Colts hadn't run a halfback option for years. How did he know? Because Wayne told him.

"He actually told me in the middle of the game," Spencer said. "Right after they scored and were about to run the two-point conversion, he said, 'Man, we ain't run that in eight or nine years.' "

Spencer said the play was his one lapse all afternoon, and he spoke like it was the one blunder that cost his team the game. The truth is that Spencer has been one of the top performers the last two weeks, and there were plenty of errors to go around.

Cornerback Dre' Bly dropped a would-be interception he could have turned into six points. Right tackle Adam Snyder allowed a sack on a crucial third-down play in the fourth quarter. And Michael Crabtree, while leading his team with 81 receiving yards, also was responsible for an interception and a fumble.

The 49ers keep getting in sight of the finish line in big games, but they end up tripping over themselves as much as they do their opponents.

Read Matthew Barrows' archives and blogs at www.sacbee.com/sf49ers.