The City captain suffered a groin strain before the tournament and missed the opening two group games.
But he replaced Thomas Vermaelen with 74 minutes on the clock and helped The Red Devils secure their third straight World Cup victory.
Adnan Januzaj scored the only goal of the game, a brilliant curling effort into the top corner that Jordan Pickford could do nothing about.
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Fabian Delph played the full 90 minutes and impressed – but John Stones came off at half-time with a suspected calf problem.
The result means Belgium top Group G and will face Japan in the last 16. That game will be played in Rostov-on-Don on Monday at 7pm.
England finish second with six points and they now face Colombia in Moscow on Tuesday.
Tunisia beat Panama 2-1, ensuring a third-place finish in Group G for the Africans.
