Shamshuddin, who infuriated England by giving Joe Root out lbw in the previous game when replays showed he got a thick inside edge, cited fitness for sitting out the series decider.
The 46-year-old, who has stood in 11 T20 internationals, will be performing the third umpire duties while his compatriot Nitin Menon will stand alongside Anil Chaudhary.
England skipper Eoin Morgan expressed "extreme frustration" at Shamshuddin's dismissal of Root in the final over in Nagpur on Sunday when India scraped a five-run victory over the tourists.
Shamshuddin also turned down an England lbw appeal against Indian skipper Virat Kohli in Nagpur. Replays later showed the ball would have hit the middle and off stumps.
First Published: February 1, 2017, 8:16 PM IST