The Padres, in the corresponding roster move, are expected to option left-hander Cesar Ramos to Portland.
Thatcher, who has been on the 15-day disabled list with a strained left shoulder since April 5 (retroactive to March 26), appeared in six games on a rehabilitation assignment with Portland.
Thatcher had a 3.60 ERA for Portland and retired the only batter he faced in a game on Wednesday on a strikeout.
Thatcher first experienced soreness in his shoulder in Spring Training. He would have made the 25-man Opening Day roster had he not been hurt.
Thatcher, 29, is coming off what qualifies as a breakout year for him. After starting last season with Triple-A Portland, on the heels of a disastrous 2008, he posted a 2.80 ERA in 52 games, holding left-handers to a .182 batting average.
Better still, Thatcher had a 1.65 ERA in 36 appearances following the All-Star break.
Ramos had a 3.86 ERA in six games with the Padres, allowing one hit in 2 1/3 innings.