Before leaving the Red Sox for good, Youkilis was lifted for a pinch-runner after hitting a triple in the seventh inning.
Youkilis was greeted with a hug near the first-base line from Nick Punto, who pinch-ran for him. He was given a lengthy standing ovation and the fans chanted "Yook."
Youkilis was part of the 2004 and '07 championships.
"It's tough because I know how hard he's played and he's given everything he has in every game he's every put on the Red Sox uniform. Sad," said second baseman Dustin Pedroia, a teammate of Youkilis since 2007.
Boston completed interleague play with a winning record for the eighth straight season (11-7).
Jason Heyward continued his torrid June for the Braves, hitting a solo homer among his three hits. Atlanta, which lost for the ninth time in 13 games, closed interleague play 8-10.
In interleague games *
At New York, Robinson Cano broke a 5-5 tie with a solo homer in the eighth inning, spoiling the Mets' rally and giving the Yankees at 6-5 victory at Citi Field.
* At Miami, Mark Buehrle (6-8) pitched effectively for seven innings to become the winningest pitcher in interleague play, John Buck hit a three-run homer and the Marlins snapped a six-game losing streak with a 9-0 win over the Toronto Blue Jays. Greg Dobbs had a two-run homer among his three hits for the Marlins, winners for just the third time in 18 games.
* At Cincinnati, Josh Willingham hit a two-run homer in the ninth off shaky closer Aroldis Chapman (4-4), rallying the Minnesota Twins over the Reds, 4-3.
* At Pittsburgh, Justin Verlander (8-4) pitched a five-hitter, Quintin Berry hit a two-run shot for his first major league home run and the Detroit Tigers beat the Pirates, 3-2.
* At Baltimore, Matt Wieters hit a two-run homer in the eighth inning to interrupt his team's agonizing offensive struggle, and the Orioles rallied to beat the Washington Nationals, 2-1.
* At Houston, Chris Johnson homered and drove in three runs and J.D. Martinez hit a two-run homer to lead the Astros to a 7-1 win over the Cleveland Indians.
* At Chicago, pinch-hitter Eduardo Escobar lined an RBI single in the 10th inning and the White Sox edged the Milwaukee Brewers, 1-0..
* At Kansas City, Carlos Beltran had three RBI and Matt Holliday and Allen Craig each had two, powering the St. Louis Cardinals to an 11-8 victory over the Royals.
* At Anaheim, Mark Trumbo drove in Albert Pujols with the tiebreaking run in the seventh inning, and the Los Angeles Angels defeated the Dodgers, 5-3.
* At San Diego, Edinson Volquez (4-7) pitched shutout ball into the seventh inning and Alexi Amarista hit a two-run double as the Padres beat the Seattle Mariners, 2-0.
* At Oakland, Derek Norris hit a three-run shot with two outs in the ninth inning for his first major league home run, and the Athletics walked off with a 4-2 win over the San Francisco Giants.
* At Arlington, Matt Harrison worked five scoreless innings for his 10th victory, Leonys Martin had a pair of extra-base hits for his first three RBI in the majors and the Texas Rangers beat Colorado, 4-2. Harrison (10-3) left the game with tightness in his lower back that caused soreness in his left hip.
In an NL game: *
At Phoenix, Wade Miley (9-3) outpitched Matt Garza (2-6) in eight strong innings, Justin Upton had three RBI and the Arizona Diamondbacks completed a three-game sweep with a 5-1 victory over the Chicago Cubs.