Van Gerwen won the last three legs to beat the Belgian, having recovered from a back problem which ruled him out of round five in Exeter and the UK Open.
Peter Wright went top of the table with a 7-5 win over James Wade, replacing Phil Taylor, who lost to Adrian Lewis.
Raymond van Barneveld beat fellow Dutchman Jelle Klaasen and Gary Anderson eased past Dave Chisnall.
World number three Wright, who won his first televised major title on Sunday in Van Gerwen's absence at the UK Open, is a point clear of the unbeaten PDC world champion.
Adrian Lewis (Eng) 7-4 Phil Taylor (Eng)
James Wade (Eng) 5-7 Peter Wright (Sco)
Kim Huybrechts (Bel) 5-7 Michael van Gerwen (Ned)
Jelle Klaasen (Ned) 5-7 Raymond van Barneveld (Ned)
Dave Chisnall (Eng) 3-7 Gary Anderson (Sco)
Michael van Gerwen marked his return from injury with a 7-5 Premier League win over Kim Huybrechts in Glasgow.