The former France striker drew the Red Bulls level in stunning fashion in the 24th minute, taking a ball from Peguy Luyindula on his chest before firing home off the crossbar from 25 yards, after Mike Magee (6) had put the Fire ahead.
Ibrahim Sekagya fired the Red Bulls ahead from close range six minutes into the second half, and further goals from Lloyd Sam (56), Eric Alexander (77) and Jonny Steele (84) added gloss, before Quincy Amarikwa scored late on for Chicago.
The result saw the Red Bulls finish one point clear of Sporting Kansas City, who won on Saturday, in both the Eastern Conference and the Supporters' Shield standing, ensuring they will be top seeds throughout the play-offs.
Juan Agudelo scored the only goal as the New England Revolution booked their place in the post-season with a 1-0 win at the Columbus Crew.
Agudelo tucked home a neat pass from Lee Nguyen in the 28th minute and the Revolution held on to ensure they will face Sporting in the play-offs next weekend.
Columbus had Domenic Oduro sent off in the last minute.
Camilo scored a hat-trick in the Vancouver Whitecaps' 3-0 win over the Colorado Rapids to end the regular season as the MLS top scorer.
The Rapids will go on to the Western Conference Knockout Game where they will face the Seattle Sounders, who drew 1-1 with the Los Angeles Galaxy.
Clint Dempsey opened the scoring on the half-hour mark, but Robbie Keane levelled for LA 12 minutes from time ensuring the Sounders ended the regular season on a seven-game winless run.
Finally the Houston Dynamo booked their play-off spot with a 2-1 win over DC United.
Oscar Boniek Garcia, with an 11th-minute penalty, and Giles Barnes (39) scored the goals for Houston in between a reply from Kyle Porter (27) for United, who finished with a record low total of three wins on the season.