Spurs boss Juande Ramos later expressed his concern for his players' safety.
The Belgian side had already been fined for crowd disturbances during a Champions League qualifier earlier in the season against Fenerbahce.
Former Genk player Zokora appeared to be hit by a lighter but was not seriously hurt, and said afterwards: "I played for four years in Belgium - and they hate me!"
Ramos said: "This is very bad for the players and those who work in football.
"But I did not see what happened. We have to be left in peace on the pitch and you can't have objects thrown because somebody could get hurt."
Spurs qualified for the knockout stage of the Uefa Cup after coming from behind to draw in Belgium.
Italian side Lazio were also fined by Uefa for the racist behaviour of fans at a Champions League Group C tie against Werder Bremen in Germany on 24 October.
Both clubs have three days to appeal against the punishment.