The Cuban had to survive a 10th round knockdown, but this was a rare scare for Rigondeaux, who added Donaire's WBO belt to his WBA title with scores of 114-113, 115-112 and 116-111.
Donaire struggled to pin down his southpaw opponent in the early rounds as Rigondeaux rattled home crisp punches before slipping out of range.
The frustrated Filipino did get through with a big left hook in the fourth round, but Rigondeaux defiantly fired back with shots of his own and Donaire was soon sporting swollen eyes.
Rigondeaux's superior speed was dictating the fight until his defences were breached in the 10th as a left hook sent him to the canvas.
Donaire desperately tried to finish off his foe, but Rigondeaux quickly regained his composure and skilfully stayed out of trouble for the remainder of the round.
This would be Donaire's best moment of the fight as Rigondeaux pressed home his advantage in the closing rounds, worsening his opponent's eye in the 11th before rocking him in the last with a big barrage.