Shkodran Mustafi's goal was cancelled out at the death as Arsenal were made to wait to qualify for the Europa League knockout stages.
The Gunners drew 1-1 in torrential rain in Guimaraes as their winning run in this year's competition came to an end.
Unai Emery made eight changes from the draw with Wolves at the weekend as he once again gave his second-string options a chance to shine.
But it was one of his regulars who made the decisive contribution for the visitors, the German rising highest to head in a free-kick late on.
However they couldn't hold on as Bruno Duarte acrobatically volleyed in in injury time to earn a share of the spoils.
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