The right-hander, out since Aug. 16 with right elbow tendinitis, made his last start on Aug. 15 at Minnesota, allowing nine runs in 3 1/3 innings.
Thomas, who'll be used primarily out of the bullpen against left-handed hitters, went 9-8 with a 4.31 ERA in 32 games combined for Tacoma and Double-A West Tennessee.
Valbuena, primarily a second baseman, split the season with Tacoma and Tennessee, hitting .301 with 11 homers, 60 RBI and 17 stolen bases in 126 games.
The Mariners also transferred infielder/outfielder Mike Morse from the 15-day to the 60-day disabled list. Morse has been out since April 29 with a separated right shoulder. He has resumed baseball activity, but won't be cleared to play until next season.