The 20-year-old Fitzpatrick, chasing his maiden victory on the tour, posted a six-under-par 64 for a 12-under tally of 198, the same total as overnight leader Willett (71).
Frenchman Raphael Jacquelin (68) was in third place on 200, one ahead of defending champion David Lipsky (69) of the United States.
"I didn't get off to the best of starts with a bogey at the first," former world amateur number one Fitzpatrick told reporters in the Swiss Alps. "At that point 74 was looking much more likely than 64.
"I made a couple of good up and downs to save par at the start of the round which just helps keep the momentum going. Then I got going with a birdie on four and carried it on from there."
Former world number one Lee Westwood (68), 10th-ranked Sergio Garcia (66) and number 18 Patrick Reed (69) were all down the field on 205, five under.
(Writing by Tony Jimenez; Editing by Ken Ferris)
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