The hosts headed into the match two points behind Sporting but looked on as their opponents moved into third thanks to substitute Junya Tanaka netting the decisive goal in the fifth minute of added time.
Sporting are 10 points behind leaders Benfica, who are six clear of nearest rivals Porto.
Gil Vicente's Jander and Penafiel's Davi Nkumu - the latter for two bookings inside 38 minutes - had already been sent off by the time Rabiola put the visitors ahead in the final minute of the first half.
Joao Vilela levelled from a 54th-minute penalty that came after Penafiel goalkeeper Julio Coelho received his marching orders.
Simeon Nwankwo completed the turnaround, although Gil Vicente had to hold out without Ruben Ribeiro - the midfielder's second caution arriving four minutes from time.
Boavista led thanks to Leozinho's third-minute effort but had Afonso Figueiredo red-carded in the closing stages.
