Fans of the Belgian side lit flares and threw seats at West Ham supporters during the game at London Stadium, which ended in a 2-1 win for the hosts.
UEFA said it had decided to "to fine RSC Anderlecht €50,000 (£43,600) and to ban RSC Anderlecht from selling tickets to its away supporters for the next two UEFA competition matches, for lighting of fireworks, throwing of objects, acts of damage and crowd disturbances".
The ban on ticket sales for the second game is suspended for two years.
Anderlecht are third in Group B with four points from as many games, eight points adrift of leaders West Ham.