Fulham midfielder Steve Sidwell cancelled out Paulinho's 35th-minute opener for Tottenham, but second-half goals from Harry Kane and Younes Kaboul gave Tim Sherwood's side all three points.
Sidwell had an opportunity to get his team back into the game with 13 minutes remaining, but after Christian Eriksen had been penalised for handball, he saw his penalty parried by Hugo Lloris.
Champions League qualification remains unlikely for Spurs, who are four points below fourth-place Arsenal, having played a game more, but they are now six points above Manchester United in the battle for a Europa League berth.
Fulham had won their previous two games and despite Magath making five changes to his starting XI, their momentum did not seem to be affected as they took the game to their hosts at a sunny White Hart Lane.
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The home side stepped things up around the half-hour mark, however, and after visiting goalkeeper David Stockdale had palmed an Aaron Lennon volley onto the post, Spurs went ahead.