The Kia Tigers selected Yoon with the first pick in the second round of the 2005 Korea Baseball Organization (KBO) draft.

In his rookie season, he showed signs of promise, with a 4.29 earned run average (ERA) in 84 innings pitched across 53 games as the Tigers' primary setup man.

In 2007, Yoon joined the starting rotation due to the Tigers' ace Han Ki-joo's transition to a closing pitcher.

In 2008, Yoon emerged as one of the most consistent pitchers in the KBO league, going 14–5 with a 2.33 ERA and 119 strikeouts in 154+2⁄3 innings pitched.

Yoon baffled the South American major league all-star squad, allowing only two runs and seven hits in 6+1⁄3 innings pitched.

In the beginning of the 2009 KBO season, Yoon became the Tigers' closer again as Han Ki-joo was put on the disabled list.

However, he had the worst pitching performance in his pro career on September 5, allowing 10 runs in 3+1⁄3 innings against the Doosan Bears, and was then sidelined with a shoulder injury for the rest of the season.

He is the first pitcher to stand at top of four categories since Korean pitching legend, Sun Dong-yeol accomplished the feat in 1991.

A free agent after the 2013 season, Yoon announced his intentions to play in Major League Baseball.