A late surge by Selangor FA, after East Bengal were reduced to 10 men, earned the hosts a 2-2 draw in Shah Alam, Malaysia, on Tuesday, but the result was enough for the Kolkata side to advance to the AFC Cup knockouts after nine years.
Group H leaders East Bengal (11 points) were on course for a hat-trick of wins as they took a 2-0 lead with goals from Orji Penn (23rd) and Lalrindika Ralte (54th) at the Shah Alam stadium.
But the home side made a surprise comeback following East Bengal forward Manandeep Singh's red card in the 78th minute.
Manandeep, who was substituted for Andrew Barisic, was shown the red card by Hong Kong referee N G Kail Lam, and East Bengal were reduced to 10 players.
The local outfit bounced back with goals from Abdul Shukur Bin Jushoh a minute later, while Adib Aizuddin bin Abdul Latif found the equaliser in 90+4th minute.
East Bengal still have a match left in Group H, against Vietnamese oufit Sai Gon Xuan Thanh at home on April 30.
But having garnered 11 points, the Trevor Morgan-coached side has made the pre-quarter-finals cut.
East Bengal last qualified for the AFC Cup knock-outs under Subhas Bhowmick in 2004.