Van den Brink was released from the final three months of his Glory contract on Monday and is set to link up with Indian club Churchill Brothers SC.
The 30-year-old, who notched 42 games for the Glory after 51 appearances for Gold Coast, said the uncertainty over whether his contract would be extended convinced him to look for opportunities elsewhere.
Clisby, a member of Glory's youth league team, was handed a senior contract last week and was immediately thrust into the starting line-up after van den Brink was struck down with a calf injury.
The 20-year-old performed well in last Saturday's 1-0 loss to the Brisbane Roar, with some of his long-range passes setting up good attacking chances for the Glory.
And with van den Brink now gone from the club, Clisby is set to team with Socceroo Michael Thwaite in the heart of defence for the remainder of the season.
Ferguson said he was impressed with Clisby's debut last week, and claimed the Glory simply couldn't afford to keep van den Brink.
"Once again, it's an opportunity for a player to move overseas and unfortunately we cannot compete dollar for dollar with these clubs," Ferguson said.
"It was not an easy decision but it's something we spoke about as a club, and decided Bas can move on."
Van den Brink became the third player to leave Perth this season, joining striker Billy Mehmet (Bangkok Glass FC) and young gun Jesse Makarounas (Melbourne Victory) out the door.
The ninth-placed Glory, who remain two points adrift of sixth spot, are expected to sign Argentinian playmaker Matias Cordoba in the coming days.
Perth take on last-placed Wellington at Eden Park on Saturday night.