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.
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