The Premier League says its clubs have "reluctantly but unanimously" decided not to release players for matches in red-list countries during September's international break.
Under current UK government rules, players would be forced to miss several games because of the 10-day isolation period required on return to the UK.
The Premier League said "extensive talks" had taken place with the Football Association and government "to find a solution" but that "no exemption had been granted".
It added that it "strongly supported" the move made by top-flight sides, which "will apply to nearly 60 players from 19 clubs who are due to travel to 26 red-list countries".
"Premier League clubs have always supported their players' desires to represent their countries - this is a matter of pride for all concerned," said Premier League chief executive Richard Masters.
"However, clubs have reluctantly but rightly come to the conclusion that it would be entirely unreasonable to release players under these new circumstances.
"Quarantine requirements mean that players' welfare and fitness will be significantly impacted. We understand the challenges that exist in the international match calendar and remain open to workable solutions."
The decision, the Premier League said, "follows Fifa's current position not to extend its temporary release exception for players required to quarantine on their return from international duty".
A statement also detailed that a period of quarantine would mean players being "unavailable to prepare for and play in two Premier League match rounds, a Uefa club competition matchday and the third round of the EFL Cup".
Fifa also recently extended the September and October international windows by two days in South America to enable countries to catch up on World Cup qualifiers that were postponed because of the coronavirus pandemic.
World football's governing body said the two-day extension ensured "sufficient rest and preparation time between matches".
It means matches can now be played on Thursday, 9 September and Thursday, 14 October, with players involved being released for 11 days.
At a meeting of Premier League clubs, they also "discussed their dissatisfaction" with this move, which "places additional international obligations on players from that region, to the detriment of their availability to represent their clubs".
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