The home side dominated the game at the beginning stages, creating pressure on the visiting team's defence but Abahani missed a golden opportunity to break the deadlock in the 25th minute.
Nabib Newaj Jibon took advantage of a lack of communication between Salam Ranjan Singh and Juanan but the striker failed to beat Bengaluru goalkeeper Lalthuammawia Ralte in a one-on-one situation inside the box.
Bengaluru grabbed the opening goal in the 40th minute through forward Nishu Kumar Tashni. Following a Harmanjot Khabra pass, Sunil Chhetri and Daniel Lalhlimpuia interchanged a few passes. Daniel then delivered the ball to Nishu who fired past Abahani custodian Shahidul Alam Sohel.
Abahani started to gather some rhythm after resumption. Imtiaz Sultan Jitu replaced Yeasin Khan at the hour mark. Emeka Darlington and Jonathan David Brown created some chances but poor finishing, especially from Jibon, denied them from hitting the back of the net.
Marjan Jugovic sealed victory by doubling the lead in the 82nd minute. Chhetri initiated the attack, Eugeneson Lyngdoh passed the ball to Jugovic and his shot hit the woodwork, bounced towards the ground before coming out of the goalline. The referee said the ball crossed the line.
Abahani head coach Drago Mamic made no changes to the squad that lost to Mohun Bagan earlier this month, starting with five defenders – Waly Faisal, Mamun Miah, Nasir Uddin Chowdhury, Yeasin and Rayhan Hasan.
Young midfielder Tutul Hossain Badshah also got the nod, interchanging his position with Yeasin.
The Croatian coach was once again forced to play with only two foreign players as Samad Yussif failed to make it to the plane due to visa issue. Welsh forward Jonathan played in midfield, along with Sohel Rana and Emeka with Jibon starting up front.
Abahani remained at the bottom of the Group E points table with three losses while Bengaluru expanded their lead at the summit with three straight victories.
Abahani will host Bengaluru in their fourth match on May 3.
Shahidul Alam Sohel; Waly Faisal, Yeasin Khan, Mamun Miah, Nasir Uddin Chowdhury, Kasto Kumar; Tutul Hossain Badshah, Sohel Rana, Jonathan David Brown, Emeka Darlington and Nabib Newaj Jibon.
Lalthuammawia Ralte; Salam Ranjan Singh, Juanan, John Johnson, Nishu Kumar, Lenny Rodrigues, Harmanjot Khabra, Eugeneson Lyngdoh, Sunil Chhetri, Daniel Lalhlimpuia and Seminlen Doungel.