Russell Teibert and Kei Kamara scored for Vancouver, Teibert putting the Whitecaps up in the fourth minute and Kamara grabbing the game-winner in the 78th.
Toronto had been reduced to 10 men when Gregory van der Wiel was sent off for his second yellow card before Jozy Altidore gave them a ray of hope, converting a penalty in the 73rd after a sliding Doneil Henry handled a cross from Jay Chapman.
But Kamara answered, seizing a cross from Jordon Mutch and slotting in his 14th goal of the season.
Toronto's failure to make the playoffs follows a spectacular 2017 campaign, when their 69 points were a league record as they claimed the Supporters Shield as the team topping the MLS regular-season standings and the MLS Cup playoff crown.
In other matches, the Philadelphia Union clinched a playoff berth with a 5-1 home victory over Minnesota. Fafa Picault -- newly drafted into the US squad for upcoming friendlies against Colombia and Peru -- scored twice in the first half to five the Union a 4-0 half-time edge and while Darwin Quintero spoiled the shutout bid in the 54th minnesota for the Loons, Ilsinho added a final tally for the Union in the 79th minute.
Expansion club Los Angeles FC secured their playoff berth in their first campaign, Adama Diomande's brace and Walker Zimmerman's opener giving them a 3-0 victory over the struggling Colorado Rapids.
LAFC became just the second expansion team to earn 53 points in their inaugural season. The first was current LAFC coach Bob Bradley's 1998 Chicago Fire.
Sporting Kansas City punched their playoff ticket for the seventh straight season with a 1-1 draw against the Los Angeles Galaxy.
Zlatan Ibrahimovic delivered the first goal of the match from the penalty spot -- his 21st goal of the season.
Johnny Russell grabbed the equalizer in the 83rd.
While Sporting secured their playoff berth, the draw damaged their chances of avoiding the knockout round. And the lone point left the Galaxy below the playoff line heading into the international break.
The Montreal Impact blanked visiting Columbus 3-0, moving five points ahead of D.C. United for the final Eastern Conference playoff berth but with the US capital club holding three matches in hand.