Fulham announced the departure on their website after Magath's side threw away a 3-2 lead to lose 5-3 at Nottingham Forest on Wednesday, a result which leaves them bottom of the Championship with one point from their opening seven matches.
"This is an unfortunate but necessary change," Fulham's American chairman Shahid Khan said on www.fulhamfc.com.
"I am doing what I feel is right and needed for Fulham Football Club, for today as well as tomorrow. I thank our supporters for standing by us during these most difficult of times on the pitch, and promise better days ahead."
Fulham said Under-21's boss Kit Symons had been put in temporary charge while they search for a new manager.
German Magath, 61, who took over at Fulham in February when they were bottom of the Premier League, became the second manager to depart a Championship club on Thursday after Ole Gunnar Solskjaer stepped down as Cardiff City boss.
Magath told BBC Radio 5 live after he watched his side come from 2-0 down to lead 3-2 before losing 5-3 at the City Ground: "It is a catastrophe. I have never had that before in my career and I am very sorry for our fans.
"I ask for patience from the fans. I have no doubt we can get up the table.
"We were very unlucky, we played a good game but things were not good enough for us," he added.
"We should have had a fourth goal when we were 3-2 up and the game would be done but we didn't and we made one mistake and they equalise and it revived them.
"I am very sad and think all the time about our performance and playing style."
Magath, who enjoyed a stellar playing career with Hamburg and West Germany - he scored the winning goal for Hamburg in the 1983 European Cup final against Juventus - took over at Craven Cottage from Rene Meulensteen in February.
He was the club's third manager of the season after Martin Jol had been replaced by Meulensteen in December, but despite a fine reputation as a coach in Germany which included three Bundesliga titles with Bayern Munich and Wolfsburg, he could not save Fulham from the drop after 13 seasons in the top flight.
Fulham won four of his 19 league matches in charge and are in danger of repeating the fate that befell them in the 1967-68 and 1968-69 seasons when they suffered successive relegations and plunged from the old First Division to the Third Division.
Fulham host 13th-placed Blackburn Rovers on Saturday.
(Additional reporting by Michael Hann; Editing by Alan Baldwin)
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