Manassero had an eagle on the par-5 10th and added two birdies on the back nine to finish at 16-under 272 two days before his 18th birthday.
Gregory Bourdy was second after a 67 that included eight birdies. The Frenchman charged up the leaderboard with four consecutive birdies beginning at the third hole, but he bogeyed the eighth and had a double bogey on No. 11.
McIlroy had a 69 and was third, two shots back, after a holding the second-round lead as he tried to bounce back from his Masters collapse last Sunday. Schwartzel shot a 70 and finished tied for 11th at 7-under 281.
Martin Kaymer, No. 1 in the world rankings, was eight shots back in a tie for ninth after closing with a 72.
McIlroy had four birdies and a bogey on the first 11 holes, but stumbled with a double bogey on No. 12. However, the Northern Irishman rallied with three more birdies and could have forced a playoff with another birdie on the par-5 18th, but his hopes evaporated when his second shot went too far to the right.
“Obviously at this moment I’m pretty disappointed, but it was a good week,” McIlroy said. “I started out really well and to shoot the scores I did considering the traveling is a pretty good effort. … I’m proud of myself at how I picked myself up from last week and the way I came back on the back nine today.”
Manassero, who became the European Tour’s youngest winner with his victory at last year’s Castello Masters, said it was “just fantastic” to earn another trophy before turning 18.
“It was tough,” he said. “The course is really tight and all the players were doing good and playing well. It’s just not easy to concentrate, especially to stay calm.”
McIlroy, who had to take a nearly 30-hour flight to Malaysia and arrived only a day before the tournament began, looked visibly tired during the final round, despite maintaining his smile for the huge crowd swarming around him.
However, his caddy ran out of patience when some spectators ignored the ban on taking photos while players were teeing off and asked officials to confiscate some of the cameras.
Manassero will move up to 35th in the world rankings next week. He received $416,660 for winning and became the Malaysian Open’s youngest winner.
Steele seizes lead with late charge at Texas Open
In San Antonio, PGA Tour rookie Brendan Steele birdied Nos. 17 and 18 for a 4-under 68, grabbing sole possession of the Texas Open lead after beginning the day tied with six other players for the top spot.
The 28-year-old Californian put his third shot within 15 feet on the par-5 18th, then sunk the putt for his sixth birdie — offsetting a pair of bogeys.
That late surge was enough for a one-stroke lead over another up-and-comer, second-year PGA Tour pro Cameron Tringale, who also had a 68.
Third-round winds were calmer but still blew to nearly 30 mph at times, after strong gusts Friday played a role in a second-round scoring average of 75.289, the highest on Tour since the first-round of the 2008 British Open. Strong winds are forecast once again during Sunday’s final round.
