Joseba Beitia (18') opened the scoring and Papa Babacar Diawara (65') doubled the lead for the hosts. Marcos De la Espada (71') gave his side a glimmer of hope when he reduced the deficit but could not turn the tables in favour of East Bengal.
It was a brisk start to the match with both teams firing on all cylinders right from the first whistle. Mohun Bagan gave away cheap free-kicks and the Red and Golds could have taken an early lead if they had made the most of a Lalrindika Ralte free-kick.
But after the opening 10 minutes, Mohun Bagan slowly started to take the game by the scruff of its neck. Fran Gonzalez sat deep while Joseba Beitia orchestrated the play from an advanced midfield position. The Spaniard was combining well with Nongdamba Naorem who was the livewire on the left flank. The youngster was regularly making inroads in East Bengal's defence and Kamalpreet Singh at right-back was having a torrid time containing him.
East Bengal's resistance was finally overcome when Beitia drew first blood in the 18th minute. A brilliant give-and-go between Beitia and Naorem did the trick. The Kerala Blasters loanee once again dribbled past Kamalpreet and set up Beitia who calmly put his header beyond the reach of Mawia.
The Maroon and Green brigade did not take the pedal off the gas after going ahead and started pressing for their second goal. Bagan's midfield trio of Beitia-Naorem-Suhair were running riot in midfield and East Bengal had their backs pinned on the wall.
The best chance of the half for East Bengal came on the 37th minute from a set-piece. Didika curled a free-kick which was dealt unconvincingly by Sankar. Aidara picked up a loose ball and set up Santos but the Spaniard failed to head in from close range.
It was almost against the run of play that Bagan scored their second after the restart. Beitia floated in an inch-perfect corner and Diawara rose the highest to nod it home. After going down by two goals the century-old club started attacking with more intent and purpose.
They were rewarded for their persistence in the 71st when Espada pulled one back. Edmund Lalrindika produced a defence-splitting through ball and the Spanish striker who was hardly involved in the game, made his presence felt when he rifled a shot past Sankar Roy. They came agonisingly close to finding the leveller in the 80th minute when Juan Mera's screamer crashed at the crossbar and came back to play.
East Bengal kept churning out chances but were not clinical in front of goal. The likes of Santos and Mera were getting ample opportunities to wrap their laces around the ball but wasted their chances.
With the important derby win, Mohun Bagan strengthened their grip on the top of the table with 17 points from eight matches. Menendez has a tough task ahead of him as this was East Bengal's third consecutive defeat.