Originally a starter, Benoit was moved to the bullpen part-time in the 2003 season. Since then, he had served in various relief roles, making spot starts as necessary.

In 2006, Benoit ranked in the top-10 American League relievers in strikeouts, innings pitched, and percentage of inherited runners who scored.

On January 27, 2009, Benoit underwent surgery to fix a torn rotator cuff, and missed the 2009 season.

On November 19, 2010, Benoit signed a three-year contract with the Detroit Tigers. The deal was worth $16.5 million with performance bonuses up to $1 million annually. Benoit didn’t quite replicate his outstanding 2010 season but had a solid year nonetheless, finishing with a 4–3 record, 2.95 ERA and 1.05 WHIP. He struck out 63 hitters in 61 innings, allowing just 47 hits and 20 earned runs. Benoit came on in relief in the decisive Game 5 of the American League Divisional Series against New York and recorded five crucial outs. He tight-roped out of a bases-loaded, one-out jam, giving up just one run thanks to key strikeouts of Alex Rodriguez and Nick Swisher.

In 2013, Benoit became the closer for the Detroit Tigers. He replaced José Valverde, who accepted an assignment to the Toledo Mud Hens on June 21, 2013 and was subsequently released. Joaquín successfully converted his first 22 save opportunities of the 2013 season, before blowing saves in two of his final four chances, making him 24-of-26 overall. He finished the regular season with a 2.01 ERA and a 1.03 WHIP. In the ALCS against the Boston Red Sox, Benoit gave up a game-tying grand slam home run to David Ortiz, which tied the game at 5. The Red Sox would go on to win the game 6-5, and eventually the series 4-2.

In December 2013, Benoit and the San Diego Padres agreed to a two-year contract worth $15.5 million. Benoit served as the set up man for the first half of the 2014 season, but was moved into the closer role after Huston Street was traded to the Los Angeles Angels of Anaheim. Benoit returned to the setup man role in the 2015 season, after the Padres acquired Craig Kimbrel from the Atlanta Braves in a blockbuster trade that was completed on the day before opening day of the upcoming season.

On November 12, 2015, the Padres traded Benoit to the Seattle Mariners for Enyel De Los Santos and Nelson Ward.

On July 26, 2016, the Mariners traded Benoit to the Toronto Blue Jays for pitcher Drew Storen and cash. Benoit struck out Evan Longoria to record his 1,000th career strikeout in a game against the Tampa Bay Rays on September 4. On September 26, Benoit suffered a torn left calf while rushing out of the bullpen during a bench-clearing brawl against the New York Yankees, and was declared out for the remainder of the regular season. He made 25 appearances for the Blue Jays in 2016, and posted a 0.38 ERA through 23⁄3 innings pitched.

Benoit signed a one-year, $7.5 million deal with the Philadelphia Phillies on December 6, 2016.

On April 10, 2017, Benoit was named the team’s closer to replace Jeanmar Gómez.

On July 31, 2017, the Phillies traded Benoit to the Pittsburgh Pirates for Seth McGarry.

On February 21, 2018, the Washington Nationals signed Benoit to a one-year deal. He elected free agency on October 29.