Jakubauskas was acquired by Seattle from the American Association of Independent Professional Baseball on June 13, 2007 and assigned to the Double-A West Tenn Diamond Jaxx. He struck out eight batters on August 31 against the Chattanooga Lookouts. In 16 games, three starts, Jakubauskas went 0–4 with 39 strikeouts and a 4.94 ERA in 51 innings pitched. In 2008 Jakubauskas played for three different levels in the Mariners organization, the Short-Season Everett AquaSox, the Double-A Diamond Jaxx and the Triple-A Tacoma Rainiers. He started the season in West Tennessee but was soon promoted to Tacoma on May 6. He allowed three earned run or less in all of his nine starts, while tossing at least five innings in seven games. Jakubauskas struck out a season-high eight batters twice, the first on May 31 against the Salt Lake City Bees and the other on September 1 against the Portland Beavers. He limited opponents to a.243 average, including a.196 clip against lefties. He made two stints on the disabled list, the first was from June 13 to July 2 with a strained right shoulder and the second time was July 7 from August 27 with a strained left oblique muscle. In his rehab assignment with Everett from August 22 to the 27 Jakubauskas allowed one hit and striking out seven in 2 scoreless inning on August 22 against the Salem-Keizer Volcanoes. Jakubauskas also pitched for Lara in the Venezuelan Winter League where he went 4–5 with a 5.16. On April 4, 2009 it was announced that he made the Mariners final roster. Jakubauskas won his first Major League game, coming into the game in the 4th inning replacing Ryan Rowland-Smith on April 10. Jakubauskas pitched two innings giving up two runs, but maintaining a 5–4 lead as he exited the game. The win also resulted in the first save for fellow Mariner relieverDavid Aardsma. On August 22, the Mariners purchased the contract of right-hander Randy Messenger from the minors and optioned Jakubauskas to the Triple-A Tacoma Rainiers. Jakubauskas soon made a return to Seattle and finished the season on the major league roster was 6–7 with a 5.28 ERA for the club, seeing time both as starter and reliever.
Pittsburgh Pirates
Jakubauskas was claimed off waivers by the Pittsburgh Pirates on November 20, 2009. After beginning the 2010 season as a starting pitcher with the Indianapolis Indians, he was recalled by the Pirates on April 23, and made his debut with the ball club the following night in a 5–2 defeat to the Houston Astros at Minute Maid Park. With a runner at first base and two outs in the bottom half of the first inning of that game, he was hit on the back of the head, just above the right ear, by a line drive batted by Lance Berkman. Even though he never lost consciousness, Jakubauskas suffered both a concussion and a head contusion. He was released by the team on November 4, 2010.
Baltimore Orioles
Jakubauskas signed a minor league contract with the Baltimore Orioles on February 1, 2011. He began the 2011 season with the Norfolk Tides after not making the major league roster out of spring training. He replaced the optioned Brad Bergesen after the Orioles selected his contract from the Tides on April 9. He made three relief appearances before a strained right groin sent him to the 15-day disabled list on April 18. Once activated off the disabled list, he was optioned back to the Tides on May 2. After another shuttle between Baltimore and Norfolk within a two-day span later that month, he finally began an extended stay with the Orioles when he was recalled on May 30. He earned his first win with the Orioles after pitching five shutout innings in a 4–0 victory over the Oakland Athletics at Camden Yards on June 7. It was his first start since the on-field accident in Houston the previous season. He has earned a spot on Baltimore's five-man starting rotation during the season. On October 30, he declared for free agency.
On July 7, 2012, just two days after being released by the Diamondbacks, Jakubauskas signed with the Toronto Blue Jays, and was assigned to the Double-A New Hampshire Fisher Cats. On July 26, Jakubauskas was promoted to the Jays Triple-A affiliate Las Vegas 51s. On November 3, Jakubauskas was designated a minor league free agent by Major League Baseball.
Jakubauskas signed a minor league contract with the Milwaukee Brewers on December 5, 2012. He appeared in 8 games at the Triple-A level for Milwaukee before being released.
