Suhair Vadakkepeedika's (48th) strike and an own goal from Sarthak Golui (55th) put NorthEast United ahead before SC East Bengal pulled one back in the 87th minute.
As the Kolkata derby marks its 100th year, since the Cooch Behar Cup in 1921, SC East Bengal and ATK Mohun Bagan find themselves in contrasting positions in the ISL table.
Fowler was again showcaused by the AIFF on charges of using abusive language against rival players after his side's ISL match last week.
With the draw, Hyderabad are at third spot with 24 points from 17 matches while SC EB are at ninth with 17 points from as many matches.
Goals from Matti Steinmann (6th) and Anthony Pilkington (68th) secured the victory for SCEB.
There were media reports that East Bengal had made a request to chairman of AIFF's disciplinary committee Ushanath Banerjee in relation to Fowler's suspension and fine.
East Bengal had, earlier in the day, backed Fowler and denied that he was charged for making allegedly racist remarks.
Both strikes for Bengaluru came in the first half through Cleiton Silva (12') and a Debjit Majumder own goal (45'), sealing their fourth win of the season to jump to the 6th spot on the points table.
Frustrated after East Bengal's 1-1 draw against a 10-man FC Goa in Margaon on January 29, Fowler had allegedly said the refereeing was either "anti-English or anti-East Bengal".
FC Goa now have stretched their unbeaten streak to seven games, and remained at third place with 21 points from 14 matches.
FC Goa have been unbeaten in their last six games, winning thrice, and will have momentum on their side.
The Kolkata giants displayed a fine passing game, played with intent but a momentary lapse in defence in the 27th minute cost them three points.
Majumder made a slew of saves to keep CFC at bay for more than an hour after the red-and-gold were reduced to 10 players following Ajay Chhetri's send-off in the first-half.
Chennaiyin have lost just one of their last seven matches. That seems quite impressive, but they also have had five draws, on par with their opponents SC East Bengal.
Jordan Murray put Kerala ahead in the 64th minute before Neville's stoppage-time equaliser (90+5) ensured that SCEB extended their unbeaten run to six games.
East Bengal have been on an upward curve since the two sides last met in December.
The Kolkata team is now unbeaten in their last five games, while BFC's misery continued with their fourth consecutive defeat this season.
Carles Cuadrat, who had guided Bengaluru to the title in 2018-19 season, was shown the door due to their disastrous performance this year with Moosa taking over the reins.
SC East Bengal played most part of the second half with 10 men after captain Daniel Fox was sent off in the 56th minute.
The new year brought new fortunes for debutants SC East Bengal as they finally bagged their first win in the ISL, brushing aside Odisha FC 3-1 in their last outing.
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