The Rapids started strongly and Deshorn Brown should have done better with an early effort after getting behind the Vancouver defence, but he fired his half-volley wide of the post.
The home side were handed the chance to double their lead when Brown was fouled by Nigel Reo-Coker inside the area and a penalty was awarded. Vicente Sanchez took the spot kick and fired his effort past David Ousted.
Sanchez nearly added a third for his side with a spectacular bicycle kick just before the break as he teed himself up inside the box, but Ousted was alert to make the stop low to his right.
The Whitecaps pushed late in the game to try to make a late surge for a possible comeback as Matias Laba's tried a shot at goal which was deflected, but Irwin was on hand to make a brilliant reaction stop to seal the win for the Rapids.