Swann will travel back to India in time for England's first Test in Ahmedabad starting on November 15.
His absence from the final warm-up match is a further blow to the tourists who already have fitness concerns about fast bowlers Steven Finn and Stuart Broad.
Finn has a thigh injury and Broad a bruised heel, leaving them highly unlikely to play in the four-day game against Haryana starting on Thursday.
"It puts a big question mark over them, that's fairly obvious," England batting coach Graham Gooch told Sky Sports.
"With a bruised heel it is something that can be very annoying and can take time to clear up," he added.
"You've got to see how it goes each day, whether it gets better with the rest - keep checking it and see how it comes on. There's no other way of going about it really."
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- Steven Finn
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