Two minutes into the first half injury time, Dudu gave East Bengal the lead to silence the irate fans, who kept hurling abuses at their coach Eelco Schattorie at the Vidyasagar Krirangan in the outskirts of city here.
Dudu slotted the ball into the far post after being nicely set up by Ranty Martins from a ball from Shylo Malsawntluanga.
The Shillong outfit missed a flurry of chances, Dudu doubled the tally in the 66th minute taking advantage of a defensive lapse to score infront of an open net as they brightened their prospect of a third place.
With a game in hand -- away match against Shillong Lajong FC on May 30 -- East Bengal have 29 points, one point shy of Royal Wahingdoh.
There were some ugly scenes in the second half added time when East Bengal's Malswantluanga and Densill Theobald were involved in a bust-up as both were sent off straightaway.
The day simply did not belong to Wahingdoh as they also missed a penalty when Theobald bungled from the spot in the 82nd minute and the comeback bid for the visitors was over.
This was their second successive defeat by an identical scoreline – 2-0 against Mohun Bagan in the previous outing – as the qualifiers from Shillong signed off an otherwise impressive season on a low.