Basel's 2-1 victory over Salzburg which took the Swiss club into the Europa League quarter-finals on Thursday was overshadowed when their fans threw missiles onto the field and the game was held-up.
Basel were trailing 1-0 at the time when the two teams were led off in the 30th minute at the start of a 12-minute delay.
Referee Manuel Grafe took the players off when Salzburg's Kevin Kampl was targeted by a bottle while cigarette lighters were also thrown onto the field.
Basel Marek Suchy had been red-carded in the ninth minute but Marco Streller (50 minutes) and Gaston Sauro (60) scored from second-half set pieces to cancel out Jonatan Soriano's 22nd-minute volley.
The draw for the quarter-finals takes place on Friday with the ties on April 3 and 10.