Hoey closed with a 7-under 65 to finish at 17-under 271. Damien McGrane of Ireland, who either led or shared the lead for three rounds, shot a 70 and was runner-up.
Manassero needed to win to enter the top 50 in the world rankings to make the Masters, which starts April 5. He entered the final round tied for the lead but shot a 72 for 276. He bogeyed No. 1 and double-bogeyed No. 8.
The 18-year-old Italian competed in the 2009 Masters as the British amateur champion.
"I would have loved to be going to Augusta for a first time as a professional," he said. "But I will go now to Sicily this week and concentrate on winning the Sicilian Open."
This was Hoey's fourth European Tour victory and his third in less than a year. He earned almost $160,000, lifting him from No. 65 to No. 14 on the money list.
"The golf course was very enjoyable and to shoot 67 on day two and then finish with two 65s is simply amazing," he said.
McGrane, unlike Hoey, was unable to complete his third round Saturday. He returned early Sunday to play the final eight holes before starting his final round.
"It was draining especially as I am not used to leading for three rounds," he said. "But I managed to grab second on my own. And while I am pleased with second, I am also a bit disappointed."
Defending champion David Horsey of England had a 66 for 279.