Protesters marched through Bissau's streets lined with hedges and palm trees singing and shouting "Jomav out!", using an abbreviation for the president's name. The protest followed a smaller one two weeks ago also demanding that Vaz quit.
The former Portuguese colony has not convened parliament for more than a year and public anger is growing at the failure of regionally-mediated talks to resolve deep rivalries within the political elite.
"Today people have had enough," said Armindo Gomes, one of the activists behind the protest. "We are heading right up to Jose Mario Vaz's bed to make him leave by force."
Vaz has yet to react to the protests, but he has defended his record in government and says he has cracked down on graft.
In August 2015 Vaz sacked Prime Minister Domingos Simoes Pereira, who was popular with Western donors and locals, triggering a crisis that the nomination of several prime ministers since has failed to resolve.
Diplomats fear the current crisis could be exploited by drug traffickers in a highly unstable country that has been a major transport hub for Latin American cocaine. The nation's main legal export is cashew nuts.
Guinea Bissau has witnessed nine coups or attempted coups since 1980.