Initially used mainly as a setup man, Jones soon became a closer for the Astros. His best years came with the Detroit Tigers from 1997–2001, when he logged 142 saves. On April 22, 1999, Jones earned career save number 100. On September 27, 1999, Jones threw the last official pitch at Tiger Stadium, striking out Carlos Beltrán as the Tigers defeated the Kansas City Royals 8–2.
While playing for the Colorado Rockies in April 2003, Jones made remarks criticized as anti-gay comments during a discussion of the play Take Me Out. Jones publicly apologized, but did not retract his comments.
Jones signed a one-year contract with the Florida Marlins during the 2004 offseason. After an injury to incumbent closer Guillermo Mota, Jones took on the role for the first time since being traded to the Minnesota Twins in 2001. He finished the 2005 season with a 2.10 ERA and 40 saves. On December 8, 2005, Jones signed a two-year contract to return to the Tigers. In 2006, he also participated in the inaugural World Baseball Classic.
Jones was a finesse pitcher and showed good durability. He threw a low-90s fastball as his main pitch, usually aiming for contact. In every year from the strike-shortened 1994 season to 2007, he pitched in at least 51 games. On May 21, 2006, he became the Detroit Tigers' all-time leader in saves, passing Mike Henneman. On July 27, 2008, Jones lost the closer role to Fernando Rodney. On September 25, 2008, Jones announced his retirement from Major League Baseball.
Jones is a devout Christian, and is known for using Contemporary Christian music when entering from the bullpen. During the 2006 playoffs, he entered to "Last One Standing" by MercyMe.
Since 2002, Jones has been writing a weekly column, "The Closer", for The Sporting News and Jones was on the cover of the baseball preview issue with the caption "Don't Tell columnist Todd Jones but (Beware of The Tigers)".
Jones currently resides in Pell City, Alabama with his wife Michelle and his son Alex (born 10-7-94) and daughter Abby (born 5-22-97). He currently works as an adviser for the local high school and middle school boys baseball teams. He is active in the community as a fundraiser for several charities.
Since 2012, Jones has also fronted a Jimmy Buffett tribute band called Come Monday.