Prater's 59-yarder as the first half expired gave the Broncos a 10-7 lead. It was the second-longest in team history, behind Jason Elam's 63-yarder in 1998. Prater is now 9 for 11 from 50 yards or more, the best long-distance success rate in NFL history.
The field goal was set up by rookie Syd'Quan Thompson's first career interception. Broncos linebacker Jason Hunter also recorded his first pickoff as a pro.
Prater misfired from 49 yards out in the third quarter, however, ending his streak of 18 straight conversions, one shy of Elam's team record.
Tebow, who ran six times for 23 yards and didn't attempt a pass in his first action in a month, scored his first NFL touchdown on a 5-yard scamper in the second quarter that tied it at 7.
Just two weeks ago, McDaniels labeled "ridiculous" the suggestion that Tebow, who rushed for 57 touchdowns at the University of Florida, could be the answer to the Broncos' short-yardage struggles in the red zone.
DENVER – LaDainian Tomlinson broke the Broncos' hearts again.
L.T. scored his second touchdown from 2 yards out with 73 seconds left after a pass interference flag and the New York Jets rallied past the Denver Broncos 24-20 on Sunday.
On fourth-and-6 from the Denver 48, Denver safety Renaldo Hill and Jets receiver Santonio Holmes jostled near the goal line and the ball fell incomplete as the crowd went crazy. But field judge Gary Cavaletto threw his yellow flag and called Hill, who had grabbed Holmes' face mask while falling to the turf, for pass interference.
The Broncos (2-4), who led most of the game, let Tomlinson score on the next play so they could get one last shot at the win.
A bad snap by J.D. Walton at midfield, however, was recovered by cornerback Dwight Lowery with 35 seconds left as the Jets (5-1) left Invesco Field with the best record in the AFC despite committing three turnovers after coming in with just one all season.
Tomlinson, who scored 19 touchdowns in 18 games against Denver while playing for San Diego in the AFC West, also scampered in from 20 yards out to tie it at 17 with 8 1/2 minutes remaining.
That score came after rookie Demaryius Thomas caught Kyle Orton's high pass over cornerback Darrelle Revis from 17 yards out to put Denver ahead 17-10 in the third quarter. The score was set up when safety Jim Leonhard was whistled for blasting Brandon Lloyd helmet-to-helmet just as the receiver hauled in a 29-yard pass on the sideline.
Before the big penalty on Hill, it looked as though this would be a signature win for Denver coach Josh McDaniels, who is 4-12 since beginning his rookie season with six straight wins.
Despite a depleted secondary that was missing three key players, including safety Brian Dawkins, the Broncos befuddled Jets quarterback Mark Sanchez, who threw his first two interceptions of the season and could have had two more passes picked off.
The Broncos found some balance, recording their first 100-yard rushing game of the season,Tim Tebow found the end zone for his first NFL touchdown and Matt Prater nailed a career-long 59-yard field goal and put Denver ahead 20-17 with a 48-yarder with just under four minutes left.
On fourth-and-6 from midfield, Holmes raced down the Jets sideline and fought with Hill for the pass 2 yards shy of the goal line.
Tebow, playing for the first time since a cameo appearance in the opener at Jacksonville, his hometown, took the direct snap and plowed around the right tackle for the score.
The Jets took a 7-0 lead on the first play of the second quarter when Braylon Edwards ran a post route unchecked by Champ Bailey, who often looked confused in coverage as he led a secondary that was missing starters Andre' Goodman and Brian Dawkins, and his backup, Darcel McBath, who were out with injuries.
With a bunch of replacements in the lineup, the Broncos didn't disguise coverages much but Sanchez was mostly unable to capitalize until the waning minutes.
Bailey and rookie cornerback Perrish Cox each dropped interceptions on the Jets' first two throws and then the Broncos came up empty despite starting two of its first three drives in Jets' territory.
The first one ended in Revis' recovery of a fumble by tailback Knowshon Moreno, who gained 14 yards on his first carry in a month but coughed it up.
Then, long snapper Lonnie Paxton's bad snap thwarted a 28-yard field-goal attempt after Hunter's interception at the Jets 33.
Nick Folk's 56-yarder tied it at 10 in the third quarter on a play in which the Broncos had just nine defenders.