Ze Manuel scored the only goal of the game as the visitors leapfrogged Setubal and Nacional into 12th with just their fourth win of the Portuguese top-flight season.
In a heated finale to the contest, referee Manuel Mota handed out five yellow cards from the 83rd minute onwards, including two to the hosts' Miguel Pedro, who was sent off in the fourth minute of stoppage time.
The two teams entered the match with just seven combined points from the past six rounds of matches and, with only three points separating Boavista from the relegation zone - Setubal were a point further up the table - a win was much-needed for both clubs.
It was a first-half substitute who settled matters as Ze Manuel, on in the 26th minute for the injured Anderson Correia, burst onto Leozinho's pass and placed his shot across Setubal goalkeeper Ricardo Batista and into the net.
The win took Boavista to 13 points, two ahead of Setubal, who slipped to 14th in the standings.
Boavista have a six-point gap to 17th-placed Penafiel, who occupy the final relegation spot.
