Prior to the 2006 season, the Blue Jays signed Bengie Molina as the everyday catcher, making Zaun the backup. Zaun started 2006 on the disabled list, with Jason Phillips serving as Molina’s backup during the first week of the year. Zaun hit a game-winning two-run homer off the Tampa Bay Devil Rays’ Jason Childers in his return on April 8. Molina’s struggles against right-handed pitchers caused John Gibbons to platoon the two, with Molina generally starting against left-handed pitchers and Zaun playing against righties. On September 13, 2006, he hit home runs from both sides of the plate in the same game. He was only the 4th Blue Jay in history to do this.
Because the Toronto Blue Jays actively pursued Rod Barajas of the Texas Rangers as the club’s new starting catcher during the 2006 offseason, it was assumed that Zaun would be exploring free agency as signing Barajas would mean Zaun would be maintained as a backup. Meanwhile, negotiations between Zaun and the club deteriorated, as Zaun claimed that the Jays offered “slightly better than back-up money for playing every day”. Negotiations with Barajas went as far as an offer conditional on a routine physical, but eventually fell apart for undisclosed reasons. After turning down a reported $6.5 million two-year offer from the Blue Jays a week earlier, Zaun officially accepted a two-year, $7.25 million contract offer to return to the Toronto Blue Jays as their starting catcher on November 28, 2006. The new contract deal also included a 3rd year option, guaranteed based on appearances. The signing came after Zaun was rumored to have been courted by the Boston Red Sox and New York Yankees, both in backup roles.
Arguably his most famous play with the Jays was hitting a walk-off grand slam in the bottom of the 13th inning off of Tampa Bay Rays closer Troy Percival, on September 6, 2008 with two outs in the inning, wiping out the Rays 7–4. Zaun hit only the second walk-off grand slam in Jays history but it was the first that occurred in extra innings, and even more spectacular was that his team was losing at the time, due to an RBI single by Dioner Navarro to put the Rays up 4–3 before the slam at the top of the 13th.
On January 22, 2009, Zaun signed a one-year deal with the Baltimore Orioles.
Zaun was claimed off waivers by the Tampa Bay Rays GM Andrew Friedman in exchange for Rhyne Hughes on August 7, 2009. On August 16 Zaun hit a pinch hit grand slam home run against his old team the Blue Jays in the 8th inning off Brandon League on a 3-2 fastball. On November 12, 2009 Zaun was granted Free Agency. On December 4, 2009 Zaun signed a 1 year contract with the Milwaukee Brewers for $1.9 million. After suffering a severe injury, Zaun’s 2010 season ended. In his contract with Milwaukee they have the option to pick him up for another season, his option was declined on November 2. His at-bat music is “Limelight” by Rush.
In January, Zaun signed a minor league deal with the San Diego Padres, with an invitation to spring training.
Zaun retired on March 7, 2011.
Zaun started his broadcasting career after the Blue Jays closed out their 2006 season. Throughout the playoffs, Zaun would offer his thoughts on how the teams and players were doing, and how he thought they could improve. He worked alongside Jamie Campbell on Rogers Sportsnet. He has continued to work on Sportsnet’s post-season broadcast through 2010.
After his retirement, on March 14, 2011 Zaun signed a two year contract with Rogers Sportsnet to become their studio MLB analyst. He will also serve as a part-time analyst on Sportsnet Radio Fan 590 and the Blue Jays Radio Network.
On May 10-11, 2011 Zaun filled in as the color commentator on the NESN broadcast of a Red Sox series against the Blue Jays when the normal broadcaster, Jerry Remy was ill.