England were always on the backfoot following the 15th minute dismissal of goalkeeper Robert Green for a professional foul on Artem Milevskiy and, although Andriy Shevchenko smashed the resulting penalty off the post, Serhiy Nazarenko's shot diverted into the net off Ashley Cole to win it 1-0.
The result sees Ukraine jump above Croatia, who did not play today, into second place in Group Six.
Both teams have one game left to play, with Ukraine strongly favoured as they travel to play group whipping boys Andorra on Wednesday.
Croatia face a Kazakhstan side thrashed 4-0 today in Belarus.
Timofei Kalachev scored twice for the hosts with Maksim Bordachev and Leonid Kovel also getting on the scoresheet.
The result was vindication for home coach Bernd Stange's decision to omit several big-name players, including Stuttgart star Alexander Hleb, brother Vyacheslav and BATE Borisov midfielder Igor Stasevich, in an attempt to look to the future.