In May 2012, he signed a minor league deal with the Atlanta Braves. He appeared in 26 games, going 5–0 with a 3.15 ERA and 58 strikeouts over 45 innings. In 2013, he pitched for the Mississippi Braves. He started 13 of 39 total games, finishing with a 2.76 ERA and 123 strikeouts over innings. Thomas was a nonroster invitee to 2014 Spring training with the Braves where he pitched 10.1 innings in 11 Spring training games for a 1-0 record, 2.61 ERA, 13 strikeouts, and a 1.16 WHIP. He was not expected to make the parent club, anticipating AAA Gwinnett as his 2014 team. However, due to a rash of injuries to Braves' pitchers and an impressive Spring training run, Thomas was one of the final two players named to the Atlanta Braves' Opening Day roster. He was filling a relief role with the club. On May 4, 2014, Thomas was optioned to Triple-A Gwinnett to make room for Gavin Floyd, who was activated off the disabled list. He was moved to the starting rotation in Gwinnett where he made one start, not allowing any runs in three innings and striking out five. The Braves tasked the lefty with developing a slider to add to his arsenal, strengthening his value to the Braves when they need him again. On May 10, 2014, he was recalled to Atlanta to replace Jordan Walden, who was placed on the 15-day DL for a pulled hamstring. He was expected to remain with Atlanta until May 20. He was optioned back to Gwinnett on May 31. Thomas was invited to spring training in 2015, and reassigned to Gwinnett on March 9. Thomas was recalled on April 21, a day after Andrew McKirahan was suspended for eighty games.
Los Angeles Dodgers
On May 27, 2015, he was traded to the Los Angeles Dodgers in exchange for Juan Uribe and Chris Withrow. The Dodgers assigned him to the AAA Oklahoma City Dodgers. He was recalled by the Dodgers on June 2 to serve as the designated "26th man" for a doubleheader that day. He allowed four runs on five hits in three innings of work and was credited with the loss. He returned to the team in September and appeared in nine total games for the Dodgers, with a 4.00 ERA. In 14 games, with six starts, for Oklahoma City, he was 4–1 with a 5.74 ERA. Thomas appeared in eight games for Oklahoma City in 2016, with two starts. He was 2–0 with a 1.42 ERA However, he was shut down with a shoulder injury and spent much of the season on the disabled list. He was designated for assignment by the Dodgers on June 30, 2016, to make room for newly acquired pitcher, Bud Norris and released a few days later, on July 3.
Later career
On April 25, 2019, after several years out of professional baseball due to injuries, Thomas signed with the York Revolution of the Atlantic League of Professional Baseball. He was released on July 28.
