Pacos were beaten 2-1 at Maritimo last week - a result that ended two matches without defeat in the league.
But Paulo Fonseca's men returned to the winners' list at Estadio da Capital do Movel thanks to Jose's successful spot-kick late in the opening half of the round 25 encounter.
Boavista midfielder Bernardo Tengarrinha was shown a straight red card for a challenge on Diogo Jota inside the area in the first minute of stoppage-time and Jose coolly stepped up to convert the match-winner.
Pacos are sixth in the standings, four points behind Vitoria Guimaraes, who occupy the fifth and final European spot in Portugal's top flight.
Boavista, meanwhile, languish in 13th position, six points above the relegation zone.
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