In a stay of 384 minutes at the crease, the Bengal southpaw, who was involved in a partnership of 160 runs with Rohan Gavaskar for the sixth wicket, made 159 runs from 227 balls with 17 hits to the boundary.
Not out on 81 yesterday, Ganguly reached the milestone without much problem and was involved in another small partnership of 44 runs for seventh wicket with all-rounder Laxmi R Shukla, who made 42 runs.
Chasing the first innings of 350 of Maharashtra, despite some hiccups in Bengal camp in the initial stage of the game, the elegant left-handed batsman ensured that his team got past the rival's score.
His two partnerships with Rohan and Shukla of 160 and 44 runs respectively in the middle order helped Bengal reach a total of 378 all out and seize a small lead of 28 runs.
Fast bowler Munaf Patel was the most successful bowler for Maharashtra.
He bowled Ganguly with a beauty and then accounted for three other Bengal batsmen to have an analysis of four for 104 runs in 31.5 overs. S.R. Burkul took two wickets, while S Bahutule, A Sanklecha, R P Jadhav and Dhruv Mohan all claimed one wicket each.
Maharashtra were precariously placed in the second innings at the score of 101 for the loss of three wickets.
Both the openers Mansingh Nigde and Yogesh Pawar back in the pavilion after making 30 and 39 runs respectively. Abhijit Kale was out for zero.
Captain Hrishikesh Kanitkar was not out on 22 and Dhruv Mohan on 1. Bengal spinner Saurashis Lahiri took two wickets while one was run out.