Both Blackpool and Wolves have fallen foul of Premier League rule E.20, which states that "in every league match, each participating club shall field a full-strength team".
The league has now relaxed that rule, meaning managers will be free to choose at will from their senior squad and, if need be, their pool of 'home-grown' Under-21 talent.
A spokesman for the Premier League said: "The clubs voted at the last Premier League Annual General Meeting to modify the rule regarding clubs fielding full strength teams (E.20).
"From 2011/12 onwards the rule will allow any combination of players included in a club's 25-man squad list to be selected for a Premier League fixture.
"The 25-man squad rules do allow clubs to pick Under-21 players beyond those named in their squad list and, with this in mind, it was agreed by the clubs that it was appropriate for the rule to remain in place in order to ensure the integrity of the competition."
Blackpool were fined £25,000 last season after making 10 changes for a midweek game at Aston Villa before reverting to their previous line-up for a trip to fellow-relegation battlers West Ham.
In December 2009, before the 25-man system had been introduced, Wolves were hit with a suspended fine after making sweeping changes at Manchester United, where they lost 3-0.