Trouble broke out in the 65th minute when the penalty was awarded to visitors FC Basel after the ball struck the hand of Sion defender Reto Ziegler at point-blank range.
Sion fans, already angry over a disallowed goal minutes earlier, threw objects onto the pitch as Matias Delgado was waiting to take the penalty and the teams were led off by the referee.
FC Basel fans also let off firecrackers during the stoppage.
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When play was resumed, Delgado strode up and converted the penalty to give Basel a 1-0 win which kept them 14 points clear at the top and on course for a seventh consecutive title.
Sion thought they had taken the lead just after the hour with Ebenezer Assifuah's header but the ball was cleared by Luca Zuffi and the referee ruled it had not crossed the line.
Goal-line technology is not used in the Swiss league.
(Writing by Brian Homewood in Berne, editing by Alan Baldwin)
