The Mariners' record signing Hugo Boumous who was pulling the strings from deep released Williams via a brilliant through ball, and the latter finished with aplomb to put the icing on the cake for his side.
With the win, ATK Mohun Bagan confirmed their place in the group stage of AFC Cup's main round, which kicks off on May 18.
After beating Blue Star SC of Sri Lanka in their previous match 5-0, the Mariners put up a dominant display once again.
Gokulam Kerala, Bashundhara Kings (Bangladesh) and Maziya Sports and Recreation (Maldives) will also join ATK Mohun Bagan in group D.
Abahani Dhaka had reached the playoff stage after Club Valencia of Maldives gave them a walk-over in the preliminary match, having cited financial crisis.