The hometown fans didn't like the imperfect ending one bit.
With Manning and a handful of other key players standing on the sideline hoping to save the Colts (14-1) from yet another second-half deficit Sunday, Caldwell never gave them a chance.
The New York Jets ended the Colts' pursuit of perfection and their NFL-record 23-game winning streak with a 29-15 victory that had fans serenading Lucas Oil Stadium with boos and Manning, the three-time MVP, offering support for his coach's decision.
"Until any player in here is the head coach, you follow orders and you follow them with all of your heart," Manning said. "That's what we've done as players. We follow orders. Our orders were not to give up a turnover, not to give up a kick return for a touchdown. There's not many games, under any circumstances, that you win when you have turnovers and give up a kick return for a touchdown."
The victory was more significant to the Jets (8-7), who took control of their playoff destiny with the victory, and would make the postseason for the first time since 2006 with a win next week at home against AFC North champion Cincinnati.
But for the Colts, it marked the end to a historic quest they had insisted was not a priority.
Only one other team -- the 2007 New England Patriots -- had gone 15-0 in the regular season. Only two other teams, the Patriots and 1972 Miami Dolphins had ever gone into the playoffs with a perfect record.
Don Shula's Dolphins are still the only NFL team to go an entire season undefeated, and he congratulated the Colts on their attempt at a perfect season.
"While the Jets' win today ended Indianapolis' streak and showed once again how difficult it is to go undefeated, I want to congratulate the Colts on a great run," he said. "Peyton Manning proved once again this season why he is one of the best quarterbacks in the history of the NFL and it was certainly no surprise to see him lead the Colts to an NFL-record 23 straight victories."
Manning was 14 of 21 for 192 yards, playing long enough to join Brett Favre, Dan Marino and John Elway as the only members of the 50,000-yard club.
Caldwell, players and team president Bill Polian, however, said perfection was never the goal; winning the Super Bowl was. And on Sunday, they showed exactly what they meant.
The first-year coach pulled Manning & Co. with a 15-10 lead and 5:36 left in the third quarter.
Stunned fans didn't react immediately, but when Curtis Painter, Manning's replacement, returned to the field for his second series, the boos began. They grew louder when Painter was hit by linebacker Calvin Pace and lost the ball, with Marques Douglas recovering and scoring. A 2-point conversion pass from Mark Sanchez to Dustin Keller made it 18-15 and put the Colts hopes in jeopardy.
Jets coach Rex Ryan, who joked earlier this week that he hoped the Colts rested their starters, got his wish.
"Indianapolis earned the right to do whatever they want," he said. "That's a heck of a football team. We were just going to line up and play, one way or the other. Whoever was in a Colts uniform was who we were going to play against."
The Jets sealed it with two fourth-quarter scores -- Jay Feely's 43-yard field goal and Thomas Jones' 1-yard TD run -- and afterward, the fans who stuck around booed loudly again as the players shook hands.
It was an odd response for a team that wrapped up home-field advantage in the playoffs, won more games in this decade than any team in any decade (115), broke the Patriots' previous record for longest winning streak (21) and had won a franchise-record 13 straight home games.
"I don't blame them a bit, man," three-time Pro Bowl center Jeff Saturday said. "I probably would have booed, too. I don't blame them. They pay to come see us win games, and we didn't get it done."
New York took advantage of the opportunity.
The Colts' downfall began when Brad Smith fielded Pat McAfee's kick to start the second half six yards into the end zone, ran it out, found a seam along the right side and raced down the sidelines. He even managed to stay in bounds after getting hit at about the Colts 20, going 106 yards to give the Jets a 10-9 lead.
It was the longest return in Jets history and tied for the second-longest in NFL history with three others. Only Ellis Hobbs' 108-yard kickoff return against the Jets in 2007 was longer.
But the Colts came right back. They moved 81 yards, the last coming when Donald Brown bounced off two Jets defenders and scooted into the end zone to make it 15-10 with 10:13 left in the third quarter. Brown's conversion run failed.
"Football logic has to come into play, and that logic is it makes no sense to have guys out there with the potential for injuries," Polian said. "We played for 16 weeks, sharp as any team in football. The good thing is that none of this mattered in the standings."
- Colts owner Jim Irsay honored longtime offensive line coach Howard Mudd before the game. Mudd retired briefly this spring, then returned during the summer and said this would be his final season.
- Clark caught four passes for 57 yards to go over 1,000 yards for the season.
- Jones ran 23 times for 105 yards, putting him within 12 yards of his career high.
- Sanchez was 12 of 19 for 106 yards, but threw no interceptions.