Neymar and Kylian Mbappe cleverly combined in the 22nd minute to allow Messi to curl home and become the first player to score against 40 teams in the Champions League.
However, Danilo Pereira awkwardly sent Enzo Fernandez's cross into his own net to restore parity at Estadio da Luz.
Though PSG had the better second-half chances, manager Christophe Galtier missed the chance to become the third coach in club history to win his first three Champions League games, though his side remain top of Group H on goals scored.
Gianluigi Donnarumma was the busier of the two goalkeepers early on, making important stops to deny Goncalo Ramos and David Neres as Benfica shaded the early exchanges.
Yet it was PSG which took the lead, its fearsome attacking trident combing before Messi combined curled a delightful finish into the left-hand corner to make it 1-0.
Benfica was level just before half-time, as Fernandez's teasing cross was skewed into his own net by Pereira.
PSG hit the woodwork just after the interval, Neymar skimming an overhead kick off the top of the crossbar after Odisseas Vlachodimos parried Achraf Hakimi's shot.
Benfica's goalkeeper denied Neymar and Hakimi again, but saved his best stop for last when he prevented Kylian Mbappe's long-range effort finding the top corner.