The Red Bulls spotted the Fire a 1-0 lead on Mike Magee's seventh goal of the season in the 6th minute, but then rattled off five straight scores.
Thierry Henry forged a 1-1 tie in the 24th, and the Red Bulls grabbed the lead for good shortly after halftime when Sekagya knocked in a rebound after Sean Johnson made an initial save on Henry's header.
Lloyd Sam, Eric Alexander and Jonathan Steele added late goals for New York (17-9-8), which ended with the best record in the MLS and secured the top seed in the playoffs for the first time in franchise history.
Quincy Amarikwa scored for the Fire (14-13-7), who fell out of playoff contention on the final day of the season.
Swim Week Miami Beach 2014 [PHOTOS]