The former Ryder Cup player, who was part of Europe's victorious 2010 team, has plunged down the world rankings from a career high 14th that same year to 274 today.
Now largely injury free, the 32-year-old sunk five birdies on his opening eight holes of Dubai's Majlis course before a bogey at his ninth dragged him back to four-under at the turn.
Molinari then chipped in from 35 yards to eagle his 11th hole and picked up one more shot to end two strokes behind leader Rory McIlroy's 63.
The last time the Italian scored 65 was at the Andalucía Open in March 2012 and on Thursday he credited swing coach Sean Foley for his resurgence.
"I have been working with Sean for more than a year and I think my driving is the best it's ever been - I'm very confident ... every hole is a birdie hole," Molinari told reporters, having reached 12 out of 14 fairways from the tee.
He had surgery on his left wrist in June 2012 before another operation on his left thumb last August. The two injuries were unrelated.
"The thumb is probably 90 percent, it still bothers me sometimes, but I haven't been taking painkillers for 3-4 weeks now - it's very hard to be patient, but that's another big help from working with Sean, he's helped my game and my attitude on and off the course," said Molinari, whose younger brother Francesco is the world number 43.
"In the last two years I haven't been able to play much, so the first goal will be to play a full season. If I make it back to top 50 in Europe that would be satisfying."
Molinari was one of the few players on Dubai's first-round leader board to tee off in the afternoon and on Friday the schedule will be reversed, which the Italian believes could be an advantage as he gets to play on the softer morning greens before the desert sun bakes the turf.
"The greens will be firmer and firmer as the week goes by," he added.
(Reporting by Matt Smith, editing by Pritha Sarkar)
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