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The club from Torres Vedras, a city west of Lisbon, had previously reached the cup final only once before, losing to Porto in 1956.
With this achievement, Torreense will compete in the UEFA Europa League next season.
Its historic campaign could become even more remarkable, as the team still has the second leg of its promotion play-off to play after drawing the first leg 0-0 against Casa Pia on Thursday.
Torreense took the lead after just three minutes through Mali’s Kévin Zohi before Colombia’s Luis Suarez equalised for Sporting in the 53rd minute.
Normal time ended 1-1, sending the match into extra time. Sporting then suffered a major setback when Uruguayan forward Maximiliano Araujo was sent off in the 109th minute after conceding a penalty.
Cape Verde international Stopira converted the spot-kick in the 113th minute to score the winner and deliver Torreense its first title.
Stopira, who carries the nickname in tribute to former France international Yannick Stopyra, will represent Cape Verde at the World Cup in the coming weeks.