The result gave TFC a 7-4 aggregate win in the two-legged final and handed the club its third straight title and seventh overall.
Altidore was the star man on the night with his hat trick, though Giovinco set up two of those goals and scored one for himself along the way.
Toronto opened the scoring in the 39th when Altidore finished off a flick from Marky Delgado.
Five minutes later it was Giovinco's turn as he nodded home a Jonathan Osorio cross to put his side two goals to the good.
A slick finish from Altidore gave him his second of the night just after the break and he would add his third and the club's fourth of the night with a glancing header from a corner.
Kei Kamara pulled one back for Vancouver just after the hour mark and Brek Shea's goal in the 77th cut the lead in half, but Michael Bradley set up Tosaint Ricketts in the 80th to kill off any hopes of a comeback.
Rooney's heroics at the weekend made headlines, but a smooth finish when played through on goal and a stunning free kick showed that he still has plenty of class in front of goal.
The positive form has seen United close the gap on the playoff places to just six points with games in hand on the teams above them in the playoff race.
Christian Ramirez netted his first two goals for LAFC as Bob Bradley's side took a 2-0 win over Real Salt Lake.
Ramirez joined LAFC earlier in the month and opened his account for the club with a brilliant first touch and a perfect finish 13 minutes in.
He bagged his brace 17 minutes later when he turned home from close range from Eduard Atuesta's low cross.
LAFC sits three points back of Western Conference leader FC Dallas.