Kokkinakis stunned top seed Tomas Berdych to reach his first career ATP World Tour singles final with a 3-6, 7-6 (5) 6-4 victory.
It caps the 21-year-old's remarkable recovery following a recent 18-month injury layoff from singles competition.
"I showed some glimpses of good tennis this year, so to do that consistently this week in Los Cabos means a lot," Kokkinakis told the ATP Tour's official website.
"I've had great support from the fans here all week. I love it here and I'll definitely be coming back a few more times."
Querrey, who defeated world No. 1 Andy Murray on his run to the Wimbledon semifinals in July, saw off Damir Dzumhur 3-6, 6-4, 6-4 to reach the final. The second seed is hoping for a second title in Mexico this season, having beaten Rafael Nadal in Acapulco.
"I'm going to move here," Querrey said. "I really love this tournament and hope I can win both tournaments in Mexico this year."