The Twins were three games under .500 at 29-32 and five games back of Detroit the day they signed Morales, but have fallen to 46-54 and trail the Tigers by 11 games in the American League Central.
"It's disappointing, because he was a good fit," Twins general manager Terry Ryan said. "I think a lot of people were surprised we were the team that signed him. Everything was in order but we just didn't respond. I don't know what our record was at the time, but it hasn't changed much. So it's disappointing."
The Twins also recalled infielder Jorge Polanco from Class A Advanced Fort Myers to take Morales' spot on the 25-man roster. Polanco was scheduled to be promoted to Double-A New Britain on Thursday, but joined the Twins for a second time this season instead.
The switch-hitting Morales batted .234/.259/.325 with one homer, 11 doubles and 18 RBIs in 39 games with Minnesota. He's heading back to Seattle, where he hit .277/.336/.449 with 23 homers, 34 doubles and 80 RBIs last season.
Morales, who sat out the first two months of the season before signing with the Twins, is expected to join the Mariners on Friday. He is owed roughly $4.3 million the rest of the season. Morales turned down Seattle's $14.1 million qualifying offer as a free agent last offseason.
"I think he liked it here, but we've put ourselves in a position where this is going to happen," Twins manager Ron Gardenhire said. "We'll put him in the middle of a pennant race over there, which will be fun. And we'll get a big kid back here who can throw the baseball -- and one we've seen."
Pryor, 25, has made one appearance for the Mariners this season after undergoing surgery to repair a torn right latissimus dorsi muscle in August. That one appearance was against Minnesota on July 9, when he gave up one unearned run over 1 2/3 innings.
Pryor has a career 2.81 ERA in 32 innings over the past three seasons. He went 3-1 with a 3.91 ERA, 27 strikeouts and 13 walks as a rookie in 2012.
Pryor had a 4.66 ERA with 27 strikeouts and 18 walks in 31 innings at Triple-A Tacoma this year. The 6-foot-4, 245-pounder was drafted by Seattle in the fifth round of the 2010 Draft out of Tennessee Tech University.
Pryor's average fastball velocity as a rookie was 96.3 mph, but dipped to 91.7 mph in his lone appearance this year, according to Fangraphs.com. Ryan said Pryor, who is under team control through 2018, is almost all the way back from his August surgery.
"He's got a good arm -- there's no question about that," Ryan said. "He's relatively young and at Triple-A. He's had a little bit of a history of injury, which is somewhat concerning, but he's healthy now. He has stuff. It's just about keeping him on the mound."