Colorado (2-2-7) won for the first time at home since July 25, 2014, against Chivas USA. Vancouver (6-5-2) lost consecutive matches for the first time this season.
"Should have got a draw," said Whitecaps goalkeeper David Ousted. "I felt the team showed character through a tough match.
"At the end we didn't get any points, so that's the most important thing and I'm disappointed."
Pittinari's volley finish came in the 51st minute after a cleaver flick by Gabriel Torres. It was the first time this season Colorado has scored the initial goal at home.
Vancouver's Pedro Morales bent a free kick into the back of the net in the 82nd minute, but the Whitecaps were whistled for a questionable foul. Kendall Waston rolled a shot just wide in the 90th minute.
"It's a big win against one of the top teams in the league," said goalkeeper Clint Irwin, who had his fifth shutout of the season. "We're just really pleased with how we performed tonight."
There was a weather delay during halftime due to lightning in the area. Colorado had its home game last Saturday postponed because of a storm.
Vancouver had a few good scoring chances in the first half. Kekuta Manneh's shot to the upper corner was saved by an outstretched Irwin in the 17th minute. Octavio Rivero's header in the second minute of stoppage time before halftime hit the crossbar.