Sunday Chizoba Nwadialu struck for Abahani in the ninth minute before Bagan equalised through Katsumi Yusa in the 82nd minute.
The tie was inconsequential considering both teams were already out of the race to reach the knockout phase of AFC Cup.
It was a spirited comeback from Bagan, who trailed for most part of the match.
Katsumi scored the all-important goal after the team earned a penalty.
The game at the Bangabandhu National Stadium was also affected by rain.