The announcement was made by Jack Zduriencik, the Mariners' executive vice president and general manager of baseball operations.
Messenger, who has worked almost exclusively as the closer for the Rainiers this season, had a 2.86 ERA and 25 saves in 28 opportunities, striking out 40 in 56 2/3 innings.
He has big league experience dating back to 2005 with Florida and San Francisco as well as with the Mariners, for whom he had one save and a 3.55 ERA in 13 games in 2008.
Jakubauskas, a 30-year-old who made his big league debut this season, was 6-7 with a 5.28 ERA for the club, seeing time both as starter and reliever.
In a corresponding move, the Mariners released right-hander Luis Pena from the Minors to make room for Messenger on the 40-man roster.
Lisa Winston is a reporter for MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.