With the series tied at 1-1, India won the toss and chose to bowl first and fast bowler Mohammed Siraj gave the tourists the perfect start, dismissing Jonny Bairstow and Joe Root for ducks in the second over to leave England at 12-2.
Jason Roy (41) and Ben Stokes (27) steadied the ship but Pandya (4-24) struck in his first over to remove Roy and later dismissed Stokes to put the brakes on.
Moeen Ali combined with Jos Buttler for a 75-run fifth-wicket stand before he, too, was caught behind off Ravindra Jadeja.
India's bowlers used the short ball to good effect and Buttler looked shaken up when he was hit twice on the helmet by two bouncers in one over from Siraj, but the England skipper settled down and looked to push England to a competitive total.
But Pandya struck twice in the 36th over, first dismissing Liam Livingstone (27) before getting rid of Buttler (60), with both batsmen holing out to Jadeja in the deep as the all-rounder safely pouched two difficult catches near the boundary.
England failed to get going in the death overs and although Craig Overton chipped in with 32, they were bowled out as Yuzvendra Chahal (3-60) cleaned up the tail.
Indian pace bowler Jasprit Bumrah, whose 6-19 had laid the foundation for a 10-wicket victory in the first ODI, missed the decider due to a back spasm.
(Reporting by Shrivathsa Sridhar and Rohith Nair in Bengaluru; editing by Clare Fallon)
