Pandya who came into bat at number eight, scored 108 runs off just 96 balls.
His 26 runs against spinner Pushpakumara's over set a new record of most number of runs scored by an Indian in one over in Tests.
Earlier, resuming India's innings at at 329 for 6, Pandya and Wriddhiman Saha were not able to add much to their overnight partnership as Saha was caught at gully by Dilruwan Perera off Vishwa Fernando's delivery.
But they could only add 10 more runs to their overnight partnership as Saha was caught at gully off Vishwa Fernando (2-87) off the 9th ball of the morning.
Kuldeep Yadav batted decisively with Pandya on the other end to put on 62 runs partnership for the 8th wicket.
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Mohammed Shami was just able to add 8 runs and was out caught and bowled by Sandakan.
Pandya then went onto completing his century off just 86 balls and put a tenth-wicket stand of 66 with Umesh Ydadav to guide India to 487 in the first innings.
Earlier, the visitors resumed their play at the overnight score of 329 for 6.
Holding a two-nil lead after winning the first two matches by comprehensive margins, Virat Kohli and his men stand on the cusp of history, aiming to become the first Indian team to complete a whitewash in an overseas three-Test series.