Leipzig had already announced the transfer from the Austrian club but summer warm-up games in which Quaschner played for Salzburg and their opponents in a direct agreement between them made him ineligible to play for a third side in one season.
"A surprise twist in the transfer of Nils Quaschner. The 20-year-old now returns to Red Bull Salzburg," Leipzig said in a statement after receiving surprise notification from the German Football League (DFL).
The DFL informed the club of a FIFA letter that ruled the player out due his previous matches with two teams this season.
Leipzig have climbed from the fifth tier in 2009 to the second division with three promotions in five seasons. They are currently seventh and in the running to go up again.
Critics say their meteoric rise is mainly due to the cash injected by Austrian-based energy drink manufacturer Red Bull since they bought the licence of SSV Maerkenstadt in 2009.
Red Bull also owns Salzburg.
(Reporting by Karolos Grohmann; editing by Ken Ferris)
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