The 34-year-old turned jeers into deafening cheers with his goal, which came after a series of missed opportunities left home fans wondering whether Inter would get the win their performance deserved.
His worst miss came just after the hour mark as he ballooned over a sitter, a dreadful finish which came before and after failed attempts to latch on to promising balls.
Arnautovic has had a hard time since returning to Inter on loan from Bologna last summer and those misses further frustrated supporters.
However, thanks to him Simone Inzaghi’s side now take a slender lead to Madrid, where they will face Atletico in the decisive second leg on March 13.
Atletico have been a more attacking proposition this season but retreated into the dogged defensive mode more representative of Diego Simeone’s long reign in Spain.
But they could not keep Inter out and now have to overturn Tuesday’s result in order to reach the quarter-finals.
© Agence France-Presse
Photo: Twitter @StatmanDave