Nene had 24 points and 15 rebounds, and Ty Lawson scored 23 points for the Nuggets, who have lost six of eight.
The Nuggets played their second game in as many nights without their top two scorers. Carmelo Anthony (right knee contusion) and Chauncey Billups (left groin strain) were in street clothes. Billups has missed seven of the last eight games since he was hurt Dec. 16 against Houston.
Denver's rotation got even shorter when reserve forward Chris Andersen left the game with a sprained ankle midway through the second quarter and did not return.
Even without three of their top eight players, the Nuggets nearly pulled out a win. The 76ers led 105-94 with 3:12 remaining when Arron Afflalo scored five straight points to kick off a 9-0 run that cut the lead to two with 31.8 seconds left.
Andre Iguodala hit a free throw with 15.6 seconds left to make it 106-103, and Lawson's driving layup with 11 seconds left again made it a one-point game. Willie Green and Iguodala hit a foul shot each to make it 108-105 with 4.9 seconds left, and Afflalo's 3-pointer rimmed out as the 76ers escaped with their third win in four games.
The 76ers took the lead for good with a 16-0 run that spanned the third and fourth quarters. Jason Smith hit a 3-pointer as the shot clock expired to give Philadelphia an 82-76 lead, and Green followed with a jumper with 30.7 seconds left in the period.
The 76ers scored the first seven points of the fourth quarter, capped by Rodney Carney's 3-pointer, to push the lead to 91-76 with 10:16 left.
Denver, which led 76-75 with 3:14 left in the third, went 5:24 without scoring.
Philadelphia led 96-80 early in the fourth before the Nuggets rallied.
Denver led most of the first half before Philadelphia made a run at the end of the second quarter. Iverson, who had just three points in the first period, scored seven points in the final 2:16 to help Philadelphia take a 59-55 lead with 42.4 seconds left before the break.
Lawson scored the final five points of the half to give Denver a 60-59 lead.
The Nuggets hit 14 of their last 16 shots in the first quarter, including nine in a row, before Martin missed a desperation heave at the buzzer.
Afflalo, who is averaging 7.7 points a game, had nine points in the first period to help the Nuggets take a 36-27 lead heading into the second.
This was Iverson's second game in Denver since he was traded last year. He played against the Nuggets when he was with the Pistons last season. … Iverson was honored with a video tribute during a timeout in the first quarter.