The sides both drew in the UEFA Europa League on Thursday and had been inconsistent domestically in recent weeks.
However, it was the visitors who went ahead six minutes before the break at the Estadio Antonio Coimbra da Mota, courtesy of an emphatic close-range finish from Tiago Rodrigues.
After a cross from the left, which the hosts' defence failed to deal with, the midfielder took full advantage to crash an effort into the back of the net.
Guimaraes then doubled their advantage 12 minutes from time through Marco Matias, who sidefooted into an empty net after good work from Moussa Maazou.
The striker rounded home keeper Vagner before calmly rolling the ball into substitute Matias' path, who made no mistakes with a comprehensive finish.
Guimaraes' victory moves them up to seventh - a point and two places behind Estoril, who are now without a win in five home league games.
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