Thomas failed to qualify for the FedEx Cup play-offs and admitted it had been "humiliating and embarrassing" to card a second round of 81 in the US Open in June.
The two-time major winner also shot an opening 82 in the Open at Royal Liverpool, but has still been selected by Johnson ahead of the likes of Keegan Bradley and Cameron Young.
The wildcards join automatic qualifiers Scottie Scheffler, Wyndham Clark, Brian Harman, Patrick Cantlay, Max Homa and Xander Schauffele on Johnson's team, which will attempt to win on European soil for the first time since 1993.
"Justin Thomas is one of the most talented players on the PGA Tour in my opinion," Johnson said.
"He has been, without question, the heart and soul of US Ryder Cup teams, our emotional leader.
"Overall (he has) a fantastic Ryder Cup record. His passion for the Ryder Cup is very evident. In my mind he is born for this and you just don't leave JT at home."
Koepka, who is the only LIV Golf League player to make the team, slipped out of the automatic qualifying places in the final event, having finished second in the Masters and won the US PGA Championship at Oak Hill.
"A five-time major champion, he is built in my mind for the biggest of stages and there's no bigger stage than the Ryder Cup," Johnson said.