The Frenchman suffered a suspected groin issue in the second half and after moving around gingerly had to be substituted off for Juan Mata.
Ole Gunnar Solskjaer had already made two changes prior to Martial coming off, with Bruno Fernandes and Marcus Rashford replacing Donny van de Beek and Edinson Cavani at half-time.
David de Gea was left out of the squad to face the Hammers, with the knee injury he picked up in the Southampton victory last weekend still effecting him.
The Spaniard managed to play in the Paris-Saint Germain loss in midweek, but was rested for the game against David Moyes’ side at the London Stadium.
‘He played against PSG and hopefully he will be ready for Leipzig.’
United need a point against Leipzig next week to secure qualification to the Champions League round of 16.