Manotas entered in the 80th minute and scored the winner five minutes later on a header from 12 yards off a service by Zarek Valentin to give the Dynamo three wins and two ties in their past five matches.
Erik Hurtado gave Kansas City the lead in the 30th minute. Elis tied it in the 59th, a minute after entering the match.
SKC are winless in four games, including a 5-2 home loss to the Dynamo on Aug. 25.
The match, played without spectators, had a 15-minute weather delay before the kickoff.
SKC got the early lead because Hurtado was in the right spot at the right time for his second goal of the season in his first start.
Unfortunately for him, Hurtado was first to the rebound and from 6 yards had an open net.
Kansas City is the only team in MLS to score in all its regular season matches this year. SKC last scored in their first 10 matches in 2007 when the streak reached 11.
Houston forward Darwin Quintero, who assisted on both goals, got the equalizing play going with a chip to Darwin Ceren near the right post. Ceren sent a cross to the middle of the box where Elis finished his fourth goal.
First-year Dynamo coach Tab Ramos made all the right moves and Manotas came off the bench for his second goal.
Maric made two saves while SKC keeper Tim Melia made four saves.
Houston plays Wednesday at Colorado. SKC hosts Minnesota on Sept. 13.