The defender rose to meet a slick Krisztian Nemeth cross and powered a header past Vancouver goalkeeper David Ousted for his second of the season.
The Whitecaps had a chance to take sole possession of top spot in the Western Conference with a single point, but instead lost at home in Major League Soccer for the fourth time in nine games.
Kansas City (8-3-6), which is in its first season in the West, improved to 6-1-3 over its last 10 matches in MLS and is now just two points back of the Whitecaps with three games in hand.
The Whitecaps (10-8-2) were playing in front of their fans for the first time since the end of May after a five-game, six-week road trip while B.C. Place Stadium was occupied by the Women’s World Cup.
Sunday also marked the beginning of a busy summer stretch of 11 matches over the next seven weeks for Vancouver as the club competes in MLS, the Amway Canadian Championship final and the CONCACAF Champions League group stage.
After setting up Ellis’ goal, Nemeth fired a shot off the post behind Ousted in the 58th minute that stayed out before Jacob Peterson sent the rebound just wide.
Vancouver came close to tying it in the 61st when Cristian Techera blasted a shot that Kansas City goalkeeper Tim Melia blocked with his body. The ball rebounded off Sporting defender Matt Besler and was headed toward the goal, but Amadou Dia cleared the ball away.
Ousted then got a piece of Peterson’s scuffed shot in the 70th minute, before Techera stung Melia’s fingers on a free kick in the 76th.
The Whitecaps were without captain Pedro Morales and defender Pa-Modou Kah because of calf injuries. Morales sat out his fourth straight game, while Kah limped off in last weekend’s 2-1 loss at the Colorado Rapids.