Mukherjee claimed the last five wickets as Orissa slumped from 172 for three to 189 all out, chasing the challenging Bengal score of 269 and lost the match by 80 runs at the Jawaharlal Nehru Stadium.
Former India skipper Ganguly failed with the bat, scoring only five, but Bengal, after winning the toss, scored a healthy 269 for six thanks to a heroic century from stumper-batsman Anustup Majumdar (101 runs, 4x10, 6x1).
Bengal, by virtue of three wins and three bonus points, have a total of 15 points, which makes them the winner of the east zone round. Jharkhand, which still has a match left, is second with nine points, while Orissa and hosts Assam are out of the reckoning.
Orissa skipper Shiv Sundar Das scored a valiant 85 (4x10, 6x1), but his departure at 173 triggered the collapse which saw the side crushing to 189 all out.
Mukherjee took five for 26 while medium pacer Ranadeb Bose scalped two wickets.
In another match, Jharkhar handed Assam their third consecutive defeat by registering a three-wicket win.
Winning the toss at the Maligaon Railway Stadium ground, Assam were all out for 161 which the Jharkhand team overwhelmed by three wickets scoring 162 for seven in 48 overs.