The 24-year-old Lokeren defender was treated on the pitch during the first half of Monday's reserve-team game with Genk but did not recover after time in hospital on a life-support machine.
A club statement said: "The medical staff have done everything to save Gregory, but they finally had to acknowledge their impotence.
"Gregory passed away at around 16:30."
The former Belgium Under-21 international's condition had worsened since he was taken to hospital in Genk, with doctors giving him little chance of survival.
On Thursday his family agreed his life support should be switched off.
Lokeren say that the exact nature of Mertens's heart condition has yet to be established.
But he passed all pre-season health tests required by Europe's football governing body Uefa, and was judged to be one of the fittest players at his club.
He joined Lokeren in January 2014 from Cercle Brugge and played 15 league games this season, as well as featuring against Hull City in the Europa League in August.
The club statement continued: "Gregory was only one and a half years at the club, but in that short time his quiet modesty made him an indispensable person.
"Now we will have to learn to live with the loss."
Former Bolton midfielder Fabrice Muamba , who survived after suffering a cardiac arrest while playing against Tottenham in 2012, said: "Horrible news that Gregory Mertens has passed away, only 24 years old. #RIP."
Belgium and Everton forward Romelu Lukaku added: "Rest In Peace Gregory Mertens ... Gone too soon. Life is crazy sometimes man... One day you're here next day you're gone."
Lokeren's Pro League game with Westerlo will go ahead on Friday, with the club and fans preparing to pay their respects to the defender.
It is understood that the Belgium Football Federation plans to mark all matches on Friday with a minute's silence.
A club statement said: "The medical staff have done everything to save Gregory, but they finally had to acknowledge their impotence.
"Gregory passed away at around 16:30."
The former Belgium Under-21 international's condition had worsened since he was taken to hospital in Genk, with doctors giving him little chance of survival.
On Thursday his family agreed his life support should be switched off.
Lokeren say that the exact nature of Mertens's heart condition has yet to be established.
But he passed all pre-season health tests required by Europe's football governing body Uefa, and was judged to be one of the fittest players at his club.
He joined Lokeren in January 2014 from Cercle Brugge and played 15 league games this season, as well as featuring against Hull City in the Europa League in August.
The club statement continued: "Gregory was only one and a half years at the club, but in that short time his quiet modesty made him an indispensable person.
"Now we will have to learn to live with the loss."
Former Bolton midfielder Fabrice Muamba , who survived after suffering a cardiac arrest while playing against Tottenham in 2012, said: "Horrible news that Gregory Mertens has passed away, only 24 years old. #RIP."
Belgium and Everton forward Romelu Lukaku added: "Rest In Peace Gregory Mertens ... Gone too soon. Life is crazy sometimes man... One day you're here next day you're gone."
Lokeren's Pro League game with Westerlo will go ahead on Friday, with the club and fans preparing to pay their respects to the defender.
It is understood that the Belgium Football Federation plans to mark all matches on Friday with a minute's silence.