The Everton defender suffered a hamstring injury in training on Sunday which has not responded to treatment, so he has been allowed to return to his club.
It leaves Capello to decide who will replace Baines on the bench for the Group G clash.
On Sunday, Darren Bent and Micah Richards were both ruled out, so Capello now has a 22-man squad, having opted not to bring in any replacements.
The chances are Manchester City's Joleon Lescott will be drafted onto the bench as he is capable of filling the left-back role Baines was deputising for.
However, James Milner has been considered flexible enough to fill the gap in the past and that could allow for a more offensive player to be involved.
Of more intrigue will be whether Frank Lampard is offered a recall on the basis that midfield duo Gareth Barry and Scott Parker are both one booking away from being suspended for next month's pivotal clash with Montenegro in Podgorica, when Jack Wilshere will definitely be missing through injury.
No matter what the result of Tuesday night's game, England will still require a draw on October 7 to book their place at next summer's finals in Poland and Ukraine.