Alan Archibald, the Firhill club captain, is expected to take charge of the team for their Irn-Bru first division match away to Cowdenbeath on Saturday
McNamara signed a new one-year rolling contract with Thistle only six weeks ago. He had taken them to this season's Ramsdens Cup final as well as second place in the league.
The loss of McNamara and his assistant Simon Donnelly is a significant blow for Thistle, who have been one of Scotland's stand-out teams this season.
A number of their players commented on Twitter about their manager's departure. Conrad Balatoni, the defender, said: "As boys have said gonna be a big loss is the gaffer. Helped me a lot! But we will continue and do all we can to win this league."
Paul Paton, the midfielder, who has been with Thistle for nearly five years, added: "Absolutely gutted the gaffers left. Been great for me and for the club. Would love Archie [Archibald] to get the job, if he wants it . . ."