Hoey shot a 7-under 65 in the final round at the Golf du Palais Royal course to total 17-under 271.
Damien McGrane of Ireland, who either led or shared the lead for three rounds, shot a 70 to finish runner-up.
Jamie Donaldson of Wales set a course record of 61 to finish equal third, the highlight being an eagle at the last when he holed his approach shot. He was joined on 13 under by Robert Coles of England (67) and compatriot Phillip Price (69).
Manassero went into the event needing to win to break into the top 50 in the world rankings to make his pro debut at the Masters, which starts April 5. He went into the final round tied for the lead on 12 under, but faltered to shoot a 72 for a share of sixth place.
The Italian, who competed in the 2009 Masters as the British amateur champion, bogeyed No 1 and double-bogeyed No 8 to end his hopes of playing at Augusta.
Defending champion David Horsey of England hit a 66 to be tied for 14th place on 9 under.
Leading final-round scores from the Hassan II Trophy at the par-72 course in Agadir, Morocco on Sunday:
271 Michael Hoey (Britain) 74 67 65 65 274 Damien McGrane (Ireland) 65 68 71 70 275 Jamie Donaldson (Britain) 72 68 74 61
Robert Coles (Britain) 73 70 65 67
Phillip Price (Britain) 68 66 72 69 276 Edoardo Molinari (Italy) 68 70 71 67
Keith Horne (South Africa) 69 70 70 67
Matteo Manassero (Italy) 69 70 65 72 277 Ignacio Garrido (Spain) 69 71 69 68
Hennie Otto (South Africa) 69 69 70 69
Pablo Larrazabal (Spain) 74 68 67 68
James Kingston (South Africa) 70 67 70 70
Jose Manuel Lara (Spain) 70 65 70 72