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The 24-year-old, who was the top-scorer for India with a 147-ball 104 in the second innings, suffered the injury while fielding in the final session on Saturday.
The tourists lost the wicket of Ben Duckett (28) to finish on 67/1, still needing 332 to go 2-0 up in the five-match series.
After a great start to his Test career, Gill has found the going tough after moving to the number three position.
Rohit was absolutely livid as his opening partner Gill was guilty of ball watching and failed to respond to his call.
Once Pandya's exit was sure, 24-year-old opener Gill was an obvious captaincy choice.
Kohli scored a tournament-best 765 runs during the recent World Cup.
The opener returned in the final over of the innings and remained unbeaten on 80.
Gill said he was looking to bat in a compact manner without sacrificing his intent to put pressure on the Lankan outfit.
The elegant right-hander returned to the nets on Thursday and Rohit was optimistic of having his opening partner back for the tournament's most anticipated match.
The Indian opener could not fly to Delhi with his teammates because his platelet count was low and flight journey was not advisable.