SWITZERLAND 25 July 2015, (AFP) - Willett, who led the British Open at St Andrews at one stage last week, had a one-shot advantage at the start of the day.
But the 27-year-old struggled on the front nine and had two bogeys and a double-bogey in his first four holes.
Two further bogeys after the turn were wiped off with a 30-foot eagle on the 15th, before he finished on one-over-par 71 but 12-under for the tournament.
Willett, who finished sixth at the Open on Monday, said he had been unwell on Saturday.
"Golf’s not the greatest game when you’re feeling a little bit under the weather, but I won’t be using it as an excuse,” he said.
Former US Amateur champion Fitzpatrick, 20, came home in 30 for a six-under round of 64.
"I didn’t get off to the best of starts, with a bogey at the first -- at that point 74 was looking much more likely than 64,” said Fitzpatrick seeking his first European Tour title.
France's Raphael Jacquelin is two shots off the lead after a third round 68, one ahead of David Lipsky of the United States while South Korea's Seuk-hyun Baek and Y.E. Yang are four off the pace.
Leading third round scores from the EPGA European Masters on Saturday. (GBR & IRL unless stated; par 70):
198 - Danny Willett 65 62 71, Matthew Fitzpatrick 69 65 64
200 - Raphael Jacquelin (FRA) 68 64 68
201 - David Lipsky (USA) 66 66 69
202 - Seuk-hyun Baek (KOR) 65 63 74, Y.E. Yang (KOR) 65 63 74
203 - Tyrrell Hatton 65 68 70, Richard Green (AUS) 65 67 71, Pelle Edberg (SWE) 65 72 66, Gregory Havret (FRA) 63 69 71
204 - Marcus Kinhult (SWE) 65 66 73, Richie Ramsay 70 66 68, Richard McEvoy 70 66 68, Anirban Lahiri (IND) 67 67 70, Johan Carlsson (SWE) 66 68 70
205 - Marco Crespi (ITA) 68 65 72, Maximilian Kieffer (GER) 71 67 67, Renato Paratore (ITA) 71 67 67, Jazz Janewattananond (THA) 65 70 70, Sergio Garcia (ESP) 69 70 66, Alejandro Canizares (ESP) 67 68 70, Patrick Reed (USA) 67 69 69, Lee Westwood 68 69 68
206 - S.S.P Chawrasia (IND) 70 66 70, Mikko Korhonen (FIN) 70 65 71, Rikard Karlberg (SWE) 65 67 74, Edoardo Molinari (ITA) 67 68 71, Florian Fritsch (GER) 70 66 70, Jyoti Randhawa (IND) 68 70 68, Julien Quesne (FRA) 67 70 69