Pawel Adamowicz, 53, was attacked on stage in front of hundreds of people on Sunday.
He was taken to hospital for stab injuries and underwent five hours of surgery at a local hospital.
A 27-year-old with a criminal record has been arrested over the attack. Police believe he used a media pass to gain access to the stage.
Poland’s health minister on Monday confirmed Mr Adamowicz had died.
“We couldn’t win,” Lukasz Szumowski told local media, referring to the battle to save his life.
Thousands attended vigils across Polish cities on Monday evening, including in Gdansk.
President Andrzej Duda described the attack as an “evil hard to imagine”.