Molinari, with a chance to move from 12th to fifth in The Ryder Cup race, holed a 138 yard nine iron for an eagle on the tenth and then made a 20 footer for another two at the short 11th.
He was 11 under par, one ahead of both Dutchman Robert-Jan Derksen and Spaniard Alejandro Cañizares, who had just run up a bogey six on the long ninth.
Overnight leader and defending champion Martin Kaymer - he led by one after Canizares twice went in the water on the last three holes of his third round - had fallen three behind and was part of a group which also included Northern Irish star Rory McIlroy and English trio Mark Foster, Kenneth Ferrie and Danny Willett.
Molinari was joined by Derksen and Cañizares on 11 under, but Derksen incredibly put three balls in the water on the 399 yard 15th and a sextuple bogey ten went on his card.
But as that was happening Miguel Angel Jiménez had a third successive birdie on the 13th and made it a three-way tie at the top again, while McIlroy's birdies at the 15th and 17th brought him only one behind.
Ferrie also got to ten under, but bogeyed the 17th and on the last went from a bunker over the green into the lake.
McIlroy missed his 12 foot birdie attempt on the last, so set a ten under target for those left out on the course.
Jiménez, however, sank a 20 footer on the long 14th for his fourth birdie in a row and at 12 under was one ahead of Cañizares and Kaymer, Molinari having taken six on the same hole.