Young Welsh forward Jonathan David Brown gave Abahani a deserved lead in the first half before Bagan striker Jeje Lalpekhlua equalised at the stroke of half-time. Balwant Singh and former Sheikh Jamal Dhanmondi Club forward Sony Norde netted one apiece in the second half as Abahani ended the game empty handed.
The Bangladesh Premier Football League champion, despite losing a number of key players last season, enjoyed ball possession throughout the first half but failed to keep up the momentum after the break.
Croatian coach Drago Mamic brought in young midfielder Tutul Hossain Badshah while Nasir Uddin Chowdhury replaced Samad Yussif at the centre of defence. Young striker Nabib Newaj Jibon started up front alongside Jonathan Brown with Emeka Darlington on the flanks.
Abahani piled pressure on the opponent early in the game and earned six corners within the quarter-hour mark but failed to capitalise. Most of the corners were taken by Waly Faisal but none manage to threaten the opposition defence.
The visiting side continued to dominate their cross-border opponent and finally broke the deadlock in the 21st minute through Brown. Jibon drifted into the right side of the penalty area before delivering a lovely cutback to the unmarked Brown, whose first touch found the back of the net.
Bagan's first real chance came in the 27th minute and it started after Abahani goalkeeper Shahidul Alam Sohel's fumble on a Norde strike allowed Japanese winger Katsumi Yusa to shoot. Moments later, Balwant saw his shot fly over the bar after his initial effort was blocked by Yeasin Khan.
The Sky Blues went close again two minutes later when Emeka ran towards the opponent's terrain from a counter attack but Bagan defender Eduardo Ferreira made a decent tackle inside the box to stop the Nigerian forward in a one-on-one situation.
The home side made it all square in the injury time of the opening half after shaky defending from the Dhaka giant. A cross by Balwant was collected by Norde inside the box. Norde passed the ball to Jeje Lalpekhlua, who hit the net with a left-footed strike.
Balwant put the home side ahead for the first time with three minutes into the second half. Katsumi fed Balwant with a lovely effort just outside the box and the latter sent the ball home over the Abahani keeper with a left-footed shot.
Norde sealed victory three minutes before the end of stipulated time with a brilliant solo effort. The Haitian winger fooled a couple of defenders inside the box before beating Sohel to make it 3-1.
Bagan moved to second place in Group E after the victory. India-League winner Bengaluru, who defeated Maldives champion Maziya Sports and Recreration Club 1-0 on the same day, top the group with Abahani at the bottom.
Abahani will host Bagan in their last match of the group stage on May 31 this year.
Dhaka Abahani Limited
Shahidul Alam Sohel; Rayhan Hasan, Nasi Uddin Chowdhury, Mamun Miah, Yeasin Khan, Waly Faisal; Tutul Hossain Badshah, Sohel Rana, Jonathan David Brown, Emeka Darlington; Nabib Newaj Jibon.
Debjit Majumder; Sarthak Golui, Eduardo Ferreira, Kinshuk Debnath, Raju Gaikwad; Sehnaj Singh, Bikramjit Singh Sr, Katsumi Yusa, Sony Norde; Jeje Lalpekhlua, Balwant Singh.