Jack Jewsbury scored the only goal of the game after 39 minutes when he lashed home a fierce half-volley from close range.
Portland tried to rally and piled on the pressure in the second half, introducing Jamaican winger Dane Richards to try to inject some proceedings.
The Whitecaps defended confidently in a performance which belied their disappointing position near the bottom of the Western Conference.
Omar Salgado threatened to equalise in stoppage time but he could not find a way past a spirited Whitecaps side.
Portland held on for an eye-catching victory, leaving Vancouver to wait on the progress of FC Dallas later tonight to determine their post-season fate.