Portuguese striker Joao was awarded an 81st-minute goal at Estadio da Madeira, but there were doubts whether his header had actually crossed the line.
However, the linesman had no issue with the close-range header and the goal stood, allowing hosts Nacional to extend their unbeaten Primeira Liga streak to six matches.
The match-winning goal came just two minutes after Egyptian midfielder Saleh Gomaa was sent off for a second bookable offence for a rash challenge on Diogo Amado.
Gomaa has now been sent off in consecutive games for Nacional.
Nacional are ninth in the table with 28 points after 21 matches, three clear of Estoril.
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