Sacha Kljestan, who entered the game in the 76th minute, skidded a crossing pass by Ruan from the right side of the box that deflected off Nani and into the left corner of the net. It was the fourth goal of the season for the former Manchester United star.
The shutout was the second of the season for Rowe and the 18th of his MLS career.
Vancouver (1-5-2, five points) was coming in off a 1-0 home win over Los Angeles FC on Wednesday night for its first victory of the season. The Whitecaps then spent all day Thursday making the cross-country North American flight of over 2,700 miles, the second-longest trip between MLS stadiums.
Vancouver's best chance during a 0-0 first half came in the 36th minute when defender Derek Cornelius' header from the left edge of the six-yard box flew over the crossbar.
Orlando City (3-3-2, 11 points), which finished with a 10-3 edge on shots in the half, had two good scoring chances, the first on a close-in header by Lamine Sane off a cross by Nani that went over the crossbar and the second in stoppage time on a left-footed shot from the left edge of the six-yard box by Joao Moutinho that MacMath stopped.
Nani was denied on another scoring chance in the 60th minute when his hard shot from the left side was deflected by MacMath with two hands over the goal.
Vancouver's best chance came in the 72nd minute when Hwang Inboem, who scored the winner in Wednesday night's upset of LAFC, chipped a nice drop pass by Fredy Montero from the middle of the box over the goal.
Rowe then came up with a big save in the 85th minute on Yordy Reyna, who cut inside the left side of the box and drilled a shot for the far corner that Rowe stopped with a diving two-hand save, setting the stage for Nani's game-winner three minutes later.