Starting from a 1-3 deficit in their away game in March, Bengaluru, who have booked their last-16 berth, once again faltered against the table-toppers, whose attack was just too good on the day.
By the virtue of topping the group, Persipura will now host Bengaluru in the single-leg pre-quarterfinals clash.
The Blues did draw first blood via an Udanta Singh strike in the 23rd minute but the visitors soon gained ground and kept up the pace.
But the second half completely belonged to Persipura, who after a barrage of attacks found success in the 73rd minute when Indonesian medio Imanuel Wanggai took the team ahead.
Defender Ruben Karel Sanadi then cut through the Begaluru defence four minutes later to take the game away from the hosts.
