The Mariners were down to ten men in the 69th minute as Subhasish Bose saw a second yellow. Katsumi Yusa' header from a Sony Norde freekick was overturned in the 85th minute after referee CR Srikrishna adjudged him as having fouled Arindam Bhattacharya.
The home side made one solitary change to the lineup that drew against Chennai City FC, with Eugeneson Lyngdoh in for Mandar Rao Dessai.
As for the visitors, an injured Debjit Majumder made way for Shilton Paul, while Jeje Lalpekhlua started on the bench to accommodate Darryl Duffy.
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Bagan started the game as the better side as Katsumi Yusa ran riot down their right. He nearly set Balwant Singh through in the fourth minute, but Arindam Bhattacharya read it well and came out to collect it.
Both sides had settled into a rhythm as Bengaluru were trying to patiently sit and build-up play, while Bagan were going for it with a high pressing game.
A mistake by Eduardo Ferreira meant that Sunil Chhetri was through on goal in the 17th minute, but he handled the ball while winning it and the referee spotted it to Ferreira’s relief.
The high pressing game led to a few turnovers in the middle but halfway through the first half, Bagan were creating more chances than Albert Roca would have liked.
Bengaluru were resorting to taking potshots from the edge of the box, with Eugeneson Lyngdoh especially getting a few opportunities, but there was little else going on for them.
Bagan had the chance of the night right before the edge of half-time when Yusa’s out swinging freekick was met by Balwant, but Arindam punched it away.
The hosts had the lion's share of possession but it was the Green and Maroons who peppered Roca's backline and shot-stopper with an array of shots in the first half.
Five minutes into the second period and Sunil Chhetri had a rare outburst of emotions as a call for penalty was turned down after Anas Edathodika tripped the Indian national team skipper inside the box.
Sanjoy Sen had a small scare when Shilton Paul went down in an attempt to stop a free-kick slammed in from comeback man Eugeneson Lyngdoh. He required treatment for a prolonged period and the Bagan think-tank could not have afforded another goalkeeping casualty with Debjit Majumder already out.
The Blues put the foot on the gas and launched numerous attacks but were miserable in finding the back of the net. Daniel Lalhlimpuia was denied by a heroic effort from Eduardo Ferreira who dived headfirst and cleared the effort away.
As Arindam Bhattacharya forayed onto act as a sweeping goalkeeper, Roca got on CK Vineeth for Lyngdoh and soon after Bagan were a man down. Subhasish Bose who has failed to notarize his India call-up with drab performances of late rounded off the night with his second red card of the season.
The referee did well to spot Bose's stamp on Udanta's boot but played Bengaluru on advantage. Bagan were left shocked when the left-back was awarded his second yellow during the next stoppage but Sanjoy Sen kept on a brave face and ultimately brought on their best player of the season so far - Prabir Das.
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Chhetri slammed the ball into the wrong side of the net after Juanan played him inside the box in the 74th minute as Bengaluru turned to take advantage of the extra man on the field.
With the clock ticking on, Bagan could have easily gone a goal up only for the referee to be caught in another controversial decision to turn down Yusa's header.
Sony Norde's free-kick from 25 yards was perfectly launched towards the Bagan skipper who leapt and slotted the ball into the net only for the referee to blow the whistle but replays hardly showed the Japanese man impacting Arindam during his jump.
The game took on a frantic pace in the last ten minutes which included five minutes of injury time. Even the likes of Jeje Lalpekhlua and Marjan Jugovic who came on as replacements could not get the better of either goalkeeper, who stood like rocks to earn both their respective sides a point.
Both teams remained stationary on the points table but Mohun Bagan would be the drearier side in lieu of the disallowed goal and the points table.
The I-League will take a backstage for the international break but the same two teams square off at the same venue in less than 72 hours in the AFC Cup.