Jeje Lalpekhula (fifth minute), Cornell Glen (41st) and Katsumi Yusa (83rd) scored for Mohun Bagan while Yasir Hanapi struck the lone goal for Tampines Rovers in the 43rd minute.
Mohun Bagan's Haitian recruit Norde made the difference on a day Cornell Glen had a miserable run that included missing a penalty.
Trailing 1-2, the Singapore League runners-up started strongly in the second-half but before they could bring on the equaliser and take the match to extra time, Mohun Bagan's Japanese recruit Katsumi Yusa confirmed their tickets to China with his 83rd minute strike from Sony Norde's corner.
Previously, Dempo (2009, 2011), Churchill Brothers (2010), Pune FC (2014) and Bengaluru FC (2015) made exits in the first qualifying round.
Mohun Bagan will now travel to Chinese city Jinan to clash against Shandong Luneng FC in the Preliminary Stage 2 on February 2.
Shandong Luneng FC are placed third in the Chinese Super League and it will be a real challenge for Mohun Bagan to play in Jinan where the temperature is sub-zero.
This is also Mohun Bagan's first win against the Singaporean outfit against whom they drew at home and lost away in the AFC Cup in 2007.
Coach Sanjoy Sen chose to start with the in-form India forward Jeje and his spirited runs combined with Cornell Glen and Sony Norde's pace unsettled 'The Stags' defence early on.
The Haitian cleverly tackled the Singaporean outfit's
What followed was a sheer dominance from Mohun Bagan as Norde toyed with 'The Stags' defence.
Mohun Bagan, however, missed a penalty as well as a couple of golden opportunities as they held their slender lead before Glen made it 2-0.
It was Norde who missed a long ranger in the 21st minute before Glen let the team down six minutes later after being set up brilliantly by Katsumi from the right.
Continuing his miserable run, Glen missed to convert from the spot as he shot straight into the hands of Tampines Rovers goalkeeper Izwan Mahbud in the 34th minute.
Moments later, Jeje fumbled to bring up his second after being set up by Norde as Mohun Bagan struggled to convert their chances till a defensive lapse from the Singaporeans.
Norde was once again instrumental in bringing up a second goal when he dribbled past the Tampines Rovers defenders. The goalkeeper lost control and Glen this time found his act right just in front of the goalline with his tap-in.
The Stags, playing with the lone forward in the S-League top scorer Nawaz, looked to bounce back after the changeover as they had more setpiece movements but an equaliser continued to elude them.
Three minutes into the second half, the visitors almost brought on the 2-2 equaliser when Fazrul found the back of the net but only to be ruled off side.
But before the Singapore side could force an equaliser, Mohun Bagan's Japanese recruit Yusa sealed the home side's win with his powerful rightfooter after being set up by substiture Prabir Das's header from a Norde corner kick.
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