Iyer is likely to be out of action for a minimum of four months.
The India wicketkeeper-batsman was named captain of Delhi Capitals in place of the injured Shreyas Iyer for the upcoming IPL 2021 season.
Pant has seen his stock rise in recent months with match-winning knocks in Test series wins in Australia and against England at home before sealing his spot in the limited-overs side.
Iyer dislocated his left shoulder while fielding during the first ODI against England on Tuesday and he is set to undergo surgery, which will rule him out of action for a minimum four months.
Iyer may also miss the first half of the Indian Premier League where he was to lead Delhi Capitals.
The incident happened in the eighth over of the England innings when Shreyas dived to save a drive by Jonny Bairstow off Shardul Thakur.
Former Australian all-rounder Brad Hogg has called on the Indian selectors to include Rishabh Pant in India's limited-overs squads saying that the batsman's ability to play unconventional shots makes him difficult to bowl to.
The hosts' batsmen posted 374/6 in the first ODI and put the Indian bowlers to the sword once again in the second, amassing 389/4 to set up comfortable victories.
Iyer said it was team's collective effort that carried them to their maiden IPL final.
Delhi Capitals, who had won seven out of their first nine games, have now lost four on the bounce and with a match left are in danger of missing out on the play-offs with an ever deteriorating net-run-rate of minus 0.159.