The Swans had expected the 20-year-old midfielder to begin a four-month stay at the New Stadium.
But Pratley has opted for a return to Griffin Park where he spent three months last season, making 16 appearances for the League One outfit.
Fulham boss Chris Coleman would have prefered it if Pratley had gone on loan to a Championship team, but Brentford will be delighted to have the talented youngster's services for a second time.