The hosts are now winless in nine, but Arouca can afford to breathe a little easier after moving five points clear of the relegation play-off place.
First-half goals from Serginho and Roberto put the visitors in the ascendancy, but Moussa Maazou reduced the deficit before the interval to set up a tense second half.
It looked as though Vitoria Guimaraes had earned a share of the spoils when Andre Andre netted from the spot just six minutes from time.
But Simao, who was one of five Arouca players to go into the book, kept his cool to convert a 92nd-minute penalty for Pedro Emanuel's side.
They will now hope that the bottom two - Pacos de Ferriera and Olhanense - are unable to claw back some ground this weekend, with the former hosting Nacional on Saturday, while the latter face a trip to champions-elect Benfica on Sunday.
