Molinari also shot a 67, while fellow Italian Matteo Manassero had a 68 to finish third another two shots back.
Despite his convincing victory margin, the 46-year-old Jimenez nearly faltered on the back nine.
After leading by three shots going into the final round, the Spaniard extended his advantage to six as he covered his first nine holes in 4-under.
But in the space of four holes that lead was cut to just one stroke as Molinari produced birdies at the 12th and 14th holes, and then holed a 2-foot eagle putt at the par-5 15th.
With Jimenez having bogeyed the 14th, there was a chance Molinari might produce a late dash for the line for the second weekend running. He birdied the last three holes to come from behind and win the Johnnie Walker Championship last Sunday.
Jimenez, however, got up and down after hitting a tree at the par-3 16th, which Molinari bogeyed after finding a green side bunker.
The Spaniard then birdied the 17th to ensure a long awaited victory in the Swiss mountains. It was his 22nd appearance in the European Masters and his best previous finishes had been second place in 1993 and 2004.
"It was not easy," Jimenez said. "At one point I was six ahead of Edoardo, but at the 14th I missed the fairway with my drive and went into a bunker, missed the green with the third shot, and missed a putt for a par.
"That was a lot of misses and Edoardo hit two superb shots to 2 feet at the 15th where I struggled just to make par. But it feels good to win after so many visits to these mountains where not only had I finished second twice but also been in contention many times. So I really wanted to come here and win this tournament."
The 17-year-old Manassero, appearing in his sixth tournament as a professional, won $161,445, putting him over the threshold to qualify for his first full European Tour playing card in 2011.
"I am now a full member of the European Tour for the first time, which is great,: he said. "It has been my goal since I turned professional earlier this year, something I wanted to do and making my card is fantastic."
South Korea's Noh Seungyul finished fourth after a 67 took him to 13-under, three shots behind Manassero.