Interim manager Gareth Southgate said the decision was tactical and not a reflection of the forward’s form.
Rooney, who was booed by sections of the Wembley crowd during Saturday’s 2-0 win over Malta, has not started Manchester United’s past three matches.
The 30-year-old said there was “no embarrassment” in being on the bench.
Rooney will retain the captaincy but Liverpool midfielder Jordan Henderson will be the on-field skipper on Tuesday.
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