Australia will send a full-strength side to the under-23 Asian Championships next month after a tribunal found in favour of FFA's right to select key A-League players for its national teams.
An independent arbitrator, Dominic Villa, sided with head office in a decision handed down late on Friday.
The club versus country dispute was essentially decided on legal grounds.
Clubs argued that they should not have to release players for tournaments held outside of international windows, in line with FIFA statutes.
FFA successfully relied upon on the club-signed participation agreements that allow the governing body to call up players for national team duty.
"Going into today's hearing we believed that we had a strong case," FFA chief executive David Gallop said.
"It is not ideal that this Asian Football Confederation (AFC) tournament falls outside a designated FIFA international window, however, the scheduling is outside FFA's control.
"It is vital that we are able to select strong, competitive squads for these events so that we can develop the best players possible to represent Australia at senior level."
Four teams - Central Coast, Melbourne City, Western Sydney and Adelaide United - will lose three players, with Melbourne Victory, Perth Glory and Newcastle Jets also hit by at least one absentee.
They will be away for all of January should the Olyroos progress into the last four of the 16-team tournament.
Thomas Deng, who will leave a first-team position at Victory for the competition, denied an assertion from Central Coast - which brought the action on behalf of A-League clubs - that players didn't want to attend.
"It's a good opportunity for me to do well on an international stage," he said.
"It's a tough one ... I've been playing, I've only missed one game (at Victory).
"It's your national team. You have to represent your country and you have to be proud of it."
Central Coast owner Mike Charlesworth lashed out at the decision.
"This is another body blow to the A-League and its fans," he said, personally attacking FFA chairman Steven Lowy.
"We'll roll with the punches but someone has to be made accountable for the dwindling attendance and TV broadcast figures.
"Steven Lowy came to power saying that the A-league would become the FFA's priority - the engine room for football in Australia."
He also appeared to take aim at league leaders Sydney FC - one of only two Australian clubs not to have a representative in China - for avoiding youth development.
"It is clear that some A-League clubs are already signing experienced journeyman to avoid losing players at times that are outside of sanctioned FIFA windows," he said.
"The A-League should not play second fiddle to an under 23's competition in China."