The A-League's Victorian travel fiasco has come to an end, with players and staff from three clubs arriving in New South Wales from Melbourne on Saturday morning.

The approximately 120 players and staff from Melbourne Victory, Western United and Melbourne City will now head into a 14-day quarantine period before they are allowed to complete their remaining 2019-20 fixtures.

The three teams assembled at AAMI Park on Saturday before boarding a charter flight to Sydney as the border into NSW was shut down due to Victoria's coronavirus outbreak.

The interstate trip comes after two aborted attempts to leave the state earlier this week, which drew heavy criticism from the players' union and led to A-League boss Greg O'Rourke apologising and acknowledging his job may be under scrutiny.

After the botched attempts to depart coronavirus-hit Melbourne on Monday and Tuesday, the FFA received travel exemptions from the NSW Government late on Thursday.

The all-clear to fly out on Saturday was given after Western United's most recent COVID-19 swabs were cleared on Friday, ensuring all those travelling had met the health protocols to head to NSW.

Victory chief executive Trent Jacobs said in a statement on Friday the failed attempts to exit the state on Monday and Tuesday had been tough for those involved.

"The events of Monday and Tuesday night have been incredibly frustrating, and compromised our players and staff," Jacobs said.

"I would like to take this opportunity to sincerely thank our players, coaches, staff and all their families for the exceptional way in which they've handled the challenges and unknowns of this extremely stressful week.

"While our club was disappointed with what transpired, we have remained focused on working together with FFA and the Victorian clubs to find a solution."

During their quarantine period, the players will be allowed to train but cannot play any matches.

Thursday's match between Victory and Western United will have to be rearranged due to the quarantine period now being in effect.

That will mean Friday's match between leaders Sydney FC and Wellington Phoenix at Jubilee Stadium will be the first fixture played since the league was suspended in March due to the coronavirus pandemic.

At least two other early games face rescheduling — Western United's clash with City on July 20 and Western Sydney's game against Victory on July 22.

United sit sixth with six games remaining and face a jam-packed schedule, while 10th-placed Victory have five matches to go. Second-placed City have just three regular-season games left.

With a competition window that can be extended until August 30, O'Rourke said he was confident the remaining 27 regular-season fixtures and finals can still be accommodated despite the quarantine period.