The result -- thanks to Jonas's 29th league goal this season -- was cruel on lowly Boavista who had dominated the second half and squandered several good chances.
Benfica, chasing a third successive title in their first season under coach Rui Vitoria, lead the table with 67 points, two ahead of Sporting who thrashed Arouca 5-1 on Saturday.
Porto are a further four points behind in third after beating Vitoria Setubal 1-0.
Mattheus Oliveira, the 21-year-old son of former Brazil striker Bebeto, scored twice to give Estoril a 3-0 win at Academica Coimbra in another of Sunday's games.
Raul Jimenez nearly gave Benfica a 15th minute lead with a bicycle kick which was turned away by goalkeeper Mika.
But it was Boavista who looked more threatening as Benfica keeper Ederson struggled to hold Ruben Ribeiro's shot and Renato Santos fired across the face of goal early in the second half.
Luisinho side-footed over after a move down the left, then Ribeiro turned Andre Almeida inside out as he ran at the Benfica defender, only to send his effort wide of the post.
Benfica snatched the points when Carcela headed on Eliseu's long ball into the area and Jonas, recalled by Brazil this week after a four-year absence, drilled past an exasperated Mika.
"We needed a bit more creativity and we needed to be more lucid in finding the way to goal," said Vitoria. "But the champions need to have this belief and this determination."
(Writing by Brian Homewood; editing by Ken Ferris)
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