Having sacked Joao de Deus following three successive defeats at the start of the season, the club brought in Jose Mota as successor.
Mota's arrival has failed to have much of an impact, however, with the side garnering one point from matches against Pacos de Ferreira and Sporting Lisbon and Gil Vicente remain bottom of the table with that solitary point after Sunday's latest defeat.
It looked as though they might double their points tally for the season, but Anderson Carvalho's 89th-minute winner ensured Boavista snatched all three points.
Simeon Nwankwo gave Gil Vicente the lead in the third minute, only for the home side to level 12 minutes later through Philipe.
Nwankwo restored the visitors' advantage in the 56th minute, but Carvalho levelled almost immediately and then won it for Boavista late on.
Gil Vicente are now three points adrift at the bottom after 17th-placed Penafiel drew 0-0 at Moreirense, while Vitoria Setubal climbed to 10th with a 2-0 win at home over Nacional thanks to first-half goals from Jucie Lupeta and Miguel Pedro.
Maritimo continued their positive start to the campaign with a 4-0 thumping of Vitoria Guimaraes, with all four goals arriving in the first half.
Edgar Costa opened the scoring after six minutes before a brace from Fransergio and a further Moussa Maazou effort ensured the job was done by half-time.
Elsewhere, Rui Pedro's eighth-minute goal earned Academica their first win of the season with a 1-0 triumph at Arouca.
