The win took Mumbai two points clear of Hyderabad FC at the top, while Chennaiyin FC stay in seventh place, still five points off the play-off spot.
Smarting from a 0-3 reversal in Goa, ATK Mohun Bagan started on the front foot in what turned out to be a feisty first half with Boumous finding the winning strike in the 11th minute.
Mohammed Yasir scored again for the defending champions in the second half to end their winless streak against the Red Miners
Hyderabad FC extended their lead at the top of the table and grabbed their fourth consecutive clean sheet after beating Odisha FC 1-0 in the Indian Super League on Saturday
The visitors dominated the game and it was one-way traffic throughout at the Indira Gandhi Athletic Stadium
Defending champions Hyderabad FC played out an entertaining 3-3 draw with Mumbai City FC in their opening match of the Indian Super League season in Pune on Sunday.
The match ended as a 1-1 draw with Rahul KP giving Kerala the lead in the 68th-minute. Sahil Tavora found a late equaliser for Hyderabad in the 88th-minute, sending the game into extra-time.
Nita Ambani also spoke about welcoming fans back to the stadium for the final, which will be played between Kerala Blasters and Hyderabad FC later on Sunday.
Hyderabad FC put one foot in what would be their maiden final appearance after scripting a come-from-behind 3-1 win over ATK Mohun Bagan in the first-leg of the Indian Super League second semifinal in Bambolim on Saturday.
ISL: Jamshedpur FC defeated Hyderabad FC to go to pole position with 37 points from 18 matches.
Indian Super League: Hyderabad FC qualified for their maiden semifinals with a hard-fought 2-1 win over Kerala Blasters in an entertaining ISL match on Wednesday.
Sunil Chhetri's historic goal went in vain as Hyderabad FC beat Bengaluru FC 2-1 to consolidate their lead at the top of the table in the Indian Super League in Bambolimon Friday.
Indian Super League: Bartholomew Ogbeche scored a poacher's brace on either side of halftime to take him top of the charts in the ISL's all-time scorers' list and also ensure Hyderabad FC remain top of the tree with a 5-0 win over NorthEast United on Monday.
ISL: Bartholomew Ogbeche bagged a hat-trick to help Hyderabad FC cruise past SC East Bengal.
Indian Super League: Alvaro Vazquez's first-half strike proved to be decisive as Kerala Blasters ended Hyderabad FC's unbeaten run with a 1-0 win and also jumped to the top of the points table in ISL on Sunday.
ISL: Bartholomew Ogbeche scored two goals in a 6-1 win for Hyderabad FC against Odisha FC on Tuesday.
ISL: Bartholomew Ogbeche scored the equaliser for Hyderabad FC in a 1-1 draw vs SC East Bengal.
ISL: Vlagyimir Koman scored the solitary goal as Chennaiyin FC edged past Hyderabad FC on Tuesday.