The 17-year-old, playing on an invitation, upstaged his 29-year-old compatriot Edoardo Molinari, outshooting Europe's Ryder Cup wildcard by two strokes to head the field by a shot.
Manassero needs good results in the last two of nine invitations he has been given to earn his European Tour full card for next year.
He lies 127th on the money-list with only the top 115 assured of 2011 playing rights and his faultless card gave him a good chance of completing the job by becoming the tour's youngest winner.
Manassero said Molinari, whose remarkable triple-birdie finish at Gleneagles last Sunday earned him a Ryder Cup wildcard, had inspired him.
"It was a fantastic finish, three birdies to win and get a pick, you might not see it again and if you do, it won't be soon," Manassero told reporters after his 7-under-par round.
"It's fantastic that Edoardo and Francesco (the younger Molinari brother who qualified automatically) are in the team and I hope they will have a magnificent Ryder Cup. Of course, it's one of my goals. I just need a few years to gain experience."
Manassero also paid tribute to the first Italian to play Ryder Cup, 1997 Crans winner Costantino Rocca.
"Coming from Italy, we didn't know what golf was until Rocca," he added.
Finland's Mikko Ilonen and Briton Graeme Storm moved to within a stroke of Manassero.
A 66 by Edoardo Molinari — Francesco is not playing in the tournament — showed his remarkable stamina after pulling out all the stops to earn his Ryder Cup debut.
He now has a chance to be the first player on the European Tour this year to chalk up three wins.
"I'm good at getting energy back; I'm here to win again," Molinari said.
Thailand's Chapchai Nirat confidently holed a 10-footer on the last to finish in a group two shots off the lead and produce the best score by an Asian in the event co-sanctioned by the Asian Tour.
"My putting hasn't been very good but this week I changed my putter and today I did well on the greens, which are difficult," Nirat said.
"It's good for the Asian Tour to be here this week." Spain's Miguel-Angel Jimenez, the other 2010 Ryder Cup team member in Switzerland, was three strokes off the lead.
