The Kenyan captain is undergoing rehabilitation on his knee and will not travel to the Emirates.
Wanyama has been battling with a recurring knee injury since January against Barcelona during Spurs' pre-season tour of the United States. He aggravated the same knee in Spurs 3-1 win against West Ham United in the Carabao Cup.
Spurs will also miss the services of Mousa Dembele (ankle), Serge Aurier (groin), Eric Dier (appendicitis) and defender Jan Vertonghen, who is nursing a thigh injury.
Mauricio Pochettino, however, welcomed Juan Foyth and Davinson Sanchez back to training after they recovered from injuries.