Bengaluru FC re 37 points from 19 matches while Pune FC are placed second with 30 points from 18 games. Salgaocar are have equal number of points but are placed third due to inferior goal difference.
Thoi Singh (44th) gave Bengaluru the lead but Eric Brown equalised for the hosts from the spot in the 54th minute at the Kalyani Stadium encounter.
But an own goal from Dhanachandra Singh (61st) and an 89th minute strike from India captain Sunil Chhetri gave the Ashley Westwood coached side their fourth away win as they brightened their title hopes.
It was a pretty even contest during the early stages with ball possession being similar and neither side created any clear opportunity in the opening quarter but Bengaluru striker Robin Singh had to come off with an injury.
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Bengaluru started to take control after the hour mark and showed more purpose going forward. They had the first real attempt of the game when Rooney tested United SC custodian Jayanta Paul while Chhetri also had a penalty claim denied.
Bengaluru started the second half strongly but from a counter attack, the purple brigade won a penalty when Shouvik Chakraborty was brought down inside the box by Keegan Pereira and Brown converted the spot-kick to restore parity.
The table leaders raised their tempo further after conceding with Chhetri going close with a volley. The away side regained their lead just after the hour-mark when a Rooney header went into the back of the net after taking a deflection off Dhanachandra.
At the other end, United SC did create a couple of great opportunities to equalise but Waheed was wasteful while substitute Surajit Bose was also booked for diving.
Both sides made plenty of changes in the final 15 minutes with Bengaluru also losing defender John Johnson through injury.
Chhetri finally put the final nail in United coffin capitalising on an error from Dhanachandra and slotting past Paul for his 13th of the campaign.