Navarro is with the Chicago White Sox this season.
Estrada had the better of his former battery mate in the first two at-bats when they confronted each other on Wednesday night.
Navarro's third at-bat against Estrada was another story.
The White Sox catcher hammered a two-run triple to center with two out in the seventh inning and Chicago (16-6) went on to a 4-0 victory over the Blue Jays (10-13) to increase its winning streak to six games and complete a sweep of the three-game series.
"Obviously he caught me last year and he did a really good job with me," Estrada said. "I threw him a good changeup down and away and he hit it. You just tip your hat to him. There was nothing else I could I do. I got the ball exactly where I wanted it and he just hit it. He's a good hitter."
"(Estrada) pitched a great game tonight, it was a battle of pitchers," Navarro said. "I knew in that situation I needed to make something happen. I was fortunate enough to get a changeup in the strike zone and put some good wood on it."
White Sox left-hander Jose Quintana (3-1) struck out a season-high 10 in six scoreless innings and allowed five hits and three walks.
The Blue Jays were held to a total of one run over the final two games of the series after blowing a 5-1 lead and losing the opener 7-5.
"We coughed up the first game we thought we should have won," Blue Jays manager John Gibbons said. "They just outplayed us the last couple of days. Estrada was outstanding. Our old teammate got us."
"It was a great matchup," White Sox manager Robin Ventura said. "Both of those guys were battling. Both were on the ropes, you had a chance to nick something and get a run here or there for both sides. I think Q anytime he gets in a tough spot, he got a little more on it. Probably reached back and grabbed something else.
"Estrada probably took something off. Different styles going in there. But I thought both guys pitched great. We got the hits when we needed them. Getting late in the game these guys are getting confident they can push something across."
Estrada took a one-hitter into the seventh with the score tied 0-0 and allowed a leadoff single to Todd Frazier, the second hit of the game by the White Sox third baseman.
Melky Cabrera forced Frazier at second on a grounder to shortstop but avoided the double play. Brett Lawrie walked.
Avisail Garcia struck out, but Navarro tripled to center on a 2-2 pitch to give the White Sox at 2-0 lead.
Navarro, a lumbering runner, rarely hits triples.
"I filled up that zero," he said. "I always try to fill up a zero every year. I got the triple already. The next stat is a stolen base."
During a walk to Adam Eaton, Gibbons was ejected by home plate umpire John Tumpane. It was the first time Gibbons has been tossed from a game this season. Gibbons said he was protesting a check swing call to third-base umpire Alan Porter.
Eaton stole second but Jimmy Rollins flied out to end the inning.
Left-hander Zach Duke replaced Quintana and pitched a perfect seventh.
The White Sox padded their lead in the eighth against right-hander Ryan Tepera on a leadoff single by Jose Abreu, a one-out walk to Cabrera and a two-out single by Garcia.
Right-hander Nate Jones took over on the mound for the White Sox in the eighth and set the Blue Jays down in order.
Right-hander Gavin Floyd pitched the ninth for Toronto and survived a leadoff double by Jackson.
Right-hander David Robertson pitched a perfect ninth for the White Sox.
NOTES: Chicago RHP Miguel Gonzalez was optioned to Triple-A Charlotte Wednesday and RHP Daniel Webb was recalled from Charlotte. Webb, 26, was 2-1 with a 3.38 ERA and two saves with Charlotte. Gonzalez made his White Sox debut Monday and did not factor in the decision in the 7-5 Chicago win after allowing five runs and 11 hits. ... Blue Jays RHP Ryan Tepera was recalled from Triple-A Buffalo Wednesday and LHP/RHP Pat Venditte was optioned to Buffalo. ... The Blue Jays have Thursday off before opening a three-game series at Tampa Bay on Friday with RHP Aaron Sanchez (1-1, 3.33 ERA) facing Rays RHP Erasmo Ramirez (4-1, 1.40 ERA). ... The White Sox will start LHP John Danks (0-3, 6.23 ERA) Thursday at Baltimore in the opener of a four-game series against the Orioles, who will start RHP Tyler Wilson (1-0, 2.77 ERA).