Josue Sa and Hernani both scored in the final 10 minutes to give the visitors victory in Arouca - Guimaraes' fourth straight in all competitions - after the hosts had led from the 76th minute through Diego.
The three points took Rui Vitoria's Guimaraes to 23 and above Benfica (22) and Porto (21) and into first position in the Portuguese league standings, although the latter two clubs have yet to play this round.
Arouca goalkeeper Mauro Goicoechea was culpable for both of Guimaraes' goals as the visitors surged late in an attempt to salvage the match.
Goicoechea came off his line in an attempt to punch a free-kick clear in the 82nd minute but failed to make contact as Sa got his head to the ball first, looping a header over an Arouca defender on the line and into the net.
Seven minutes later and Goicoechea was again picking the ball out of his net with the Uruguayan goalkeeper parrying a long-range strike straight to Hernani, who made no mistake from six yards.
It was a disappointing finale for Arouca, who were looking for their first league win in five games.
Arouca, who went ahead when Diego got his toe to a free-kick with 14 minutes left, have just eight points this season and sit two spots above the relegation zone.
Benfica can overhaul Guimaraes with a win at Nacional on Sunday, while Porto can do the same if they triumph at Estoril.
