Tom Kalinowski and Michael Mezei, who shared the lead after round two with Will Yanagisawa, each shot 70 in the third round and share second place at minus-6.
Brian Guetz matched Ellis' 66 and jumped into a tie for fourth at 5-under-par 211. He was joined there by Joseph Lanza (70), Michael Letzig (68), Andy Matthews (69) and Michael Harris (68).
The second round was completed earlier Saturday after darkness halted play Friday night for the second straight day on the Fazio Foothills Course at Barton Creek Resort.
Ellis opened with seven consecutive pars before a birdie at the eighth got him to minus-2. He dropped in back-to-back birdies from the 11th.
The 26-year-old got to 5 under with a birdie on the par-5 15th.
Ellis closed his round with an eagle at the par-5 18th. Ellis is a tour rookie looking for his first won on the Canadian Tour.
'From number seven on I played very well,' said Ellis, who has 20 golfers within five shots of his lead. 'I knew just to stay in the tournament I would need to shoot 3 or 4 under. Fortunately, a 66 was good enough on a very demanding golf course.'
Omar Uresti, the defending champion, posted a 71 Saturday. He stands in a tie for ninth at 4-under-par 212 with Eric Wang (67), Lee Williamson (70), John Mallinger (68) and Jim Rutledge (69). Yanagisawa struggled badly in the third round as he shot a 4-over 76 to tumble into a tie for 29th at even-par 216.