Everton rallied after a passive first 45 minutes that saw them jeered off at half-time and they drew level with 15 minutes left when Chris Smalling deflected Gerard Deulofeu's cross into his own net.
As the game looked destined for extra-time, Ander Herrera's poked pass sent Martial clear and the striker showed great composure to drill a low finish past Everton keeper Joel Robles.