The 24-year-old defender had been in a critical condition after collapsing on the field 20 minutes into a reserve game against Genk on Monday.
He was given emergency treatment on the pitch before being taken to hospital where he was placed in an induced coma.
Lokeren described Mertens as "modest" and "indispensable".
"Suddenly something happens which makes us realize that football is just football. Today is such a time," said a statement by the club.
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Mertens began his career at the country's most successful club, Anderlecht, but moved to Lokeren in January last year from Cercle Bruges.
He had been capped several times by Belgium at under-21 level.
Belgium suffered the loss of another young talent in January this year when 20-year-old Junior Malanda of German Bundesliga side Wolfsburg died in a car crash.