Captain Wayne Rooney became England’s most capped player when he lined up for his country for the 116th time.
But he failed to inspire his side in a turgid opening 45 minutes.
Raheem Sterling and Harry Kane came close for the away side in the first half with Dusan Svento failing to convert perhaps the best chance of the match at the other end.
Adam Lallana hit the post in the second period after Slovakian defender Martin Skrtel was sent off for a second bookable offence.
Substitute Theo Walcott had the ball in the net in the final minute of the match but it was erroneously disallowed for offside,
England’s blushes were saved when Lallana sqeezed in a 95th-minute strike, ensuring a winning start for their new manager.
Elsewhere in the group, Lithuanian led 2-0 at half-time at home to Slovenia but were denied victory by an injury-time equaliser.