Nigerian forward Ideni Chinedu Matthew scored the match-winner for Arambagh.
With the feat, Arambagh have now 23 points with seven wins, two draws and seven losses while Chattogram Abahani have 18 points with four wins, six draws and six losses.
Arambagh are five points clear ahead of their closest rivals Sheikh Jamal, who remained in the 6th slot with their previous credit of 18 points after conceding a 1-2 defeat to bottom-placed Team BJMC on Saturday night at the same venue.
In the match, Arambagh KS started their domination within the opening minute of the game.
But the Dhaka based club remained goalless in the entire first half.
On the other hand, Chattogram Abahani Ltd produced some good chances but failed to convert goal for lack of good finishers.
After the barren first half, Chattogram Abahani Ltd came alive and put pressure on Arambagh KS.
But, Arambagh KS finally broke the deadlock in the 63rd minute and got their expected success (1-0).
Nigerian forward Ideni Chinedu Matthew buried the ball outside from the box, utilising a pass from forward Mohammad Arifur Rahman.
Chattogram Abahani tried hard to comeback in the match but failed to level the margin.
Arambagh defender Md Jalal Mia, Md Rockey and striker Paul Emile Biyaga got yellow cards due to their aggressive brand of football.
In their first-leg match on February 3, Arambagh KS defeated Chattogram Abahani Ltd by 2-0 goals at Mymensingh Stadium.
Forward Mohammad Arifur Rahman and Cameroonian striker Paul Emile Biyaga scored one goal each for Arambagh KS.