The defender rose to meet a slick Krisztian Nemeth cross after a corner kick to power 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.
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 that saw them pick up nine of a possible 15 points 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.
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.
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 towards goal, but Amadou Dia cleared the ball from danger.
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 pressed for the equalizer late, with Tim Parker's header going just wide in the 90th minute, but couldn't find a way through on the way to suffering their second straight loss.
Teams often get off to sluggish starts following long road trips, but the Whitecaps had the run of play in the first half despite failing to find the range.
Melia made a nice stop on Kekuta Manneh, who had three goals over his last four coming into Sunday, in the 11th minute before Parker's glancing header from a corner was cleared off the Sporting line by Benny Feilhaber in the 13th.
Manneh then sent Techera in on a partial break three minutes later, but Dia recovered in time to make a clean tackle with the pint-sized winger bearing down on Melia.
Notes: 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. ... Vancouver visits the Portland Timbers next weekend. Kansas City hosts the Montreal Impact.
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