John Catlin of the US and South Korea's Sungho Lee set the early pace at the Asian Tour's season-ending event with opening rounds of 66.
Molinari became the first Italian to win a major when he clinched the British Open at Carnoustie earlier this year.
The 36-year-old South African is one shot ahead of American Kurt Kitayama and Zambian Madalitso Muthiya.
American Tony Finau holed a dramatic 15-foot birdie putt in a round of 68 to finish second on 16-under par.
The world number 33 took a three-shot lead over his fellow Australian into day four of the European Tour-sanctioned event at the Royal Pines Resort on the Gold Coast, but it quickly evaporated.
Having begun the final day six strokes clear, Rai carded 69 at the par-70 course -- his worst round of the tournament -- but Fitzpatrick's 64 was not quite enough to chase down the 23-year-old.
The pair began the final day of foursomes action, where teammates take it in turns to play the same ball, with a five-stroke lead at Melbourne's Metropolitan Golf Club.
The 23-year-old, who set a course record on Friday carded a two-under par 68 in the third round.
Italy stayed in the hunt with a 66 to be joint second alongside Mexico and South Korea.
The exhibition clash lasted five hours and finished in darkness as organizers had to use flood lights to illuminate the green on the final hole.
Belgium's Thomas Pieters and Thomas Detry fired a 71 - one of only four teams to go sub-par - to be 10 under for the tournament alongside Korea's Byeong-hun and Kim Si-woo, who hit 72.
Englishman Rai held a four-stroke advantage at the top of the board over South Korea's Park Hyo-won, who also broke the previous course record with his 62.
England's Aaron Rai, Japan's Yusaku Miyazato and Jason Scrivener of Australia managed to remain on course, all carding 65 to end top of the widely-spread leaderboard at the par-70 Fanling.
They conquered the Metropolitan Golf Club in Melbourne with 10-under par 62s in opening fourball action, with Malaysia, Belgium and defending champions Denmark a stroke further back.
The Vic Open, which aims to highlight the disparity in prize money between the tours, sees men and women play concurrently off alternating tees.