The shooting happened around 2:35 a.m. at Café Quo Vadis on Bélanger Street East in the borough of St-Léonard.
The first victim, 24, suffered gunshot wounds to his upper body, while the second, 34, was hit in the lower body.
Both are in hospital in serious but stable condition.
Montreal police spokesperson Const. Anthony Cantelmi said there were two other patrons in the café who saw what happened.
The shooters fled on foot and are being sought by police.
Bélanger Street was closed between Valdombre and d'Avila streets due to the police investigation.