This was Bagan's first win over the hosts in Bengaluru.
Bengaluru dominated the proceedings till the 73rd minute, playing attacking football. Home team skipper captain Sunil Chhetri and dangerous Kim Song Yong turned out to be a threat for Bagan defence by winning aerial duels and making off the ball runs.
However, the visitors turned the tables around in he last 15 minutes when Jeje turned inside the box to kick the ball past Amrinder Singh to give Bagan the lead.
Bagan then doubled their lead through Norde who collected a pass and sent another shot past goalkepeer Amrinder in the four minute of extra time.
Bengaluru in 87th minute had a chance to reduce the margin when Len shot hit the upright after Beikho and Len combined well inside the striking circle.
Earlier, in 69th minute C K Vineeth brought down a long pass from Curtis Omolo Osano but his strike was saved by Bagan custodian Debjit.
With this win, Bagan have 14 points from six games, moving to second on the table.
