European football's governing body said in a statement that Basel had been fined for "insufficient organisation" at the Group E game on Oct. 1, a tie they lost 1-0.
Play was halted for around five minutes when four protesters wearing orange boiler suits and helmets descended on ropes that they had dropped from the St-Jakob Park stadium roof early in the match.
They waved banners reading "Gazprom, don't foul the Arctic" and "Free the Arctic 30". The protesters then hauled themselves back on to the roof while officials watched from the touchline and the match continued.
Russian authorities detained all 30 members of the pressure group who were aboard icebreaker the Arctic Sunrise when they broke up attempts to scale state-run Gazprom's Prirazlomnaya offshore oil platform on Sept. 18.
All 30 have been remanded in custody for two months. Gazprom are sponsors of the Champions League and Schalke.
UEFA's disciplinary committee also slapped a three-match ban on Celtic's Scott Brown for his red card in the Group H match at home to Barcelona.
Brown was sent off for a foul on Neymar in the second half of Barcelona's 1-0 win.