Zanotti, three times a runner-up on tour, the last time at the 2012 Irish Open, shot his second 68 to finish six-under-par and ahead of a group that included 42-year-old Dane Thomas Bjorn.
Overnight leader Hansen, another 42-year-old Dane, dropped four shots in his first 11 holes, following up his 66 with a 78 and was two over along with former world number one Martin Kaymer of Germany, who carded a 76.
Zanotti, 30, ranked 391st in the world, had four birdies and a single bogey in his round at the testing Le Golf National course, venue for the 2018 Ryder Cup.
Defending champion Marcel Siem of Germany missed the cut and others who struggled were Luke Donald and Ian Poulter, the Britons both on two over. American Matt Kuchar was three over after a 75.
After fog delayed the start for an hour, one man in early contention was Northern Ireland's Graeme McDowell. The former U.S. Open champion fired a second 69 to be four under.
McDowell, like many of the leading contenders warming up for the British Open at Muirfield this month, had missed the cut in five of his last six strokeplay events before this week.
"I'm playing this golf course the way it's supposed to be played - fairways and greens. Once you start hitting it off line it will punish you. I just have not got the putter revved up but I am well in touch and right where I need to be," McDowell said.
"It's been a rough couple of months for me. I've not been playing the kind of golf I'd like to and the key to this week was to come and get myself in the mix for the weekend and get some of the juices flowing again."