He played in Major League Baseball (MLB) for the Baltimore Orioles, Kansas City Royals, Colorado Rockies, Detroit Tigers, Pittsburgh Pirates, and San Francisco Giants from 2004 to 2010.

He split 2001 between Utica and the Single-A Kane County Cougars of the Midwest League, going a combined 6–2 with an ERA of 3.23, 51 strikeouts, 20 walks, and 78+1⁄3 innings pitched in 15 games (14 starts).

[9] On August 31, 2003, the Marlins traded Bautista and fellow minor leaguer Don Levinski to the Baltimore Orioles for veteran Jeff Conine.

[7] The Orioles assigned Bautista to the Double-A Bowie Baysox of the Eastern League, where he went 3–5 with a 4.74 ERA, 72 strikeouts, 33 walks, and 62+2⁄3 innings pitched in 14 games (13 starts) during the 2004 season.

[11] After a second relief appearance on May 27 (in which he allowed four runs in 1⁄3 of an inning) amid a three-game sweep of the Orioles by the Yankees, Bautista was sent back to Bowie.

[13] The Royals assigned Bautista to the Double-A Wichita Wranglers of the Texas League, where he went 4–3 with an ERA of 2.53, 73 strikeouts, 32 walks, and 81+2⁄3 innings pitched in 12 starts.

[9] In September, he was called up and added to the Royals' starting rotation when the team decided to go to a six-man staff to limit their pitchers' innings.

[14] He made his first major league start on September 6, allowing four runs over six innings and taking the loss in a 7–3 defeat to the Detroit Tigers.

[9][20] On August 1, the Royals traded him along with Jeremy Affeldt to the Colorado Rockies for Ryan Shealy and Scott Dohmann.

In 12 games (eight starts) with Kansas City and Colorado on the season, Bautista had an 0–3 record, a 5.62 ERA, 27 strikeouts, and 21 walks in 41+2⁄3 innings.

[24] After Bautista allowed six runs in 1⁄3 of an inning on May 13 in a 15–2 loss to the San Francisco Giants, bringing his ERA to 19.06, he was sent back to Colorado Springs.

[26] On September 12, he made his final major league start in a bullpen game, throwing two scoreless innings in a 12–0 victory over the Philadelphia Phillies.

[29] Bautista began 2008 with the Tigers in a relief role, often pitching in the eighth-inning as the "setup man" for veteran closer Todd Jones.

[1] Due to the return of Joel Zumaya from the disabled list, Bautista was designated for assignment and was traded to the Pittsburgh Pirates on June 25 for right-handed pitcher Kyle Pearson.

[1] Bautista was eligible for arbitration but the Pirates declined to tender an offer, although general manager Neal Huntington stated "We'd like to get him back.

"[37][38] On December 22, 2008, Bautista signed a minor league contract with an invitation to spring training to return to the Pirates in 2009.

[42] On January 21, 2010, Bautista signed a minor league contract with the San Francisco Giants with an invite to spring training.

[46] In his most recent major league appearance, on August 4, he allowed back-to-back home runs to Carlos González and Troy Tulowitzki in a 6–1 loss to Colorado.

[9] He did not pitch at all in the postseason for the Giants as they won the 2010 World Series; in fact, he was granted free agency during the playoffs on October 12.

[42] On December 14, 2010, Bautista signed a minor league contract with the Seattle Mariners including an invite to spring training.

[50] In 24 games with the Tacoma Rainiers of the Pacific Coast League, Bautista had a 1–2 record, a 4.21 ERA, 49 strikeouts, and 22 walks in 36+1⁄3 innings.

[51] He served as Hanwha's closer upon joining the team in 2011, posting a 3–0 record, a 2.02 ERA, 122 strikeouts, 41 walks, and 35+2⁄3 innings pitched in 27 games.

[54][55] After the 2013 season, the Eagles chose not to resign Bautista, opting to make Félix Pie and Caleb Clay the foreign players on their roster.