Play was halted for around five minutes when four protesters wearing orange boiler suits and helmets descended slowly on ropes which they had dropped from the roof after a few minutes of play.
The banners said "Gazprom, don't foul the Arctic" and "Free the Arctic 30" and had Greenpeace written at the bottom. The protesters then hauled themselves back onto 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 both the Champions League and Bundesliga club Schalke.
Basel could be disciplined for inadequate organisation after the protesters managed to get on the roof with their bulky equipment.
"With this action, the defenders of the Arctic showed the red card to the Russian sponsors of the Champions League and German club, and to their oil-drilling and dirty tricks in the Artic," said Greenpeace in a statement.
"With it's oil drilling projects, Gazprom is putting the fragile Arctic ecosystem on the line," said Nadine Berthel of Greenpeace's Arctic campaign.
"Gazprom has no experience on the high seas and is playing Russian roulette with the Arctic. The question is not if, but when, Gazprom will make history with a full-scale oil disaster in the Arctic."
