The first arrived directly from a corner, with Canterbury keeper Adam Highfield slipping, while the second was a 30-yard free kick beautifully curled into the top corner.
Canterbury had chances to get back into the game after falling behind but their efforts were continually thwarted by a combination of poor finishing and excellent goalkeeping from Danny Robinson.
They were made to pay for their profligacy midway through the second spell when Maksim Manko made the game safe, drifting past two defenders before smashing home from the edge of the area.
Canterbury grabbed a late consolation and Russell Kamo's strike was probably the pick of the goals.
However, it wasn't enough to prevent a disappointing end to their season.
Auckland will be hoping to avoid such disappointment when their semifinal tie against Waitakere begins at Fred Taylor Park next weekend, with the O-League champions aiming to win back the trophy they last claimed in 2009.