The Padres receive 22-year-old Minor League pitcher Evan Scribner, although it wasn't the compensation that kept the deal from being done sooner.
The Padres and Diamondbacks were waiting to see if the 36-year-old Clark would waive the $500,000 assignment bonus he would have received in a trade.
Clark, a San Diego native, did and now he's a Diamondback once again.
"I've shared with a number of people within the organization how thankful I am to have had the opportunity to play for the team that I grew up idolizing," Clark said. "[General manager Kevin Towers] KT and [manager] Buddy [Black] in particular have been tremendous during my time there, and I can't say enough about them."
Clark flew with the Padres from San Diego to St. Louis Wednesday night, but then flew to Phoenix for a team workout at Chase Field on Thursday. Clark makes his home in Phoenix in the offseason.
Clark, who signed a one-year deal with the Padres just before the start of Spring Training for $900,000, is hitting .239 with one home run and 11 RBIs in 88 at-bats this season for a team that is 21 games under .500 heading into Thursday's game in St. Louis.
The trade means more playing time for 31-year-old Brian Myrow, who was promoted to the Padres from Triple-A Portland before the All-Star break. That playing time, however, will likely be in the form of pinch-hitting considering the Padres' first baseman is All-Star Adrian Gonzalez.
Clark was the Padres' best pinch-hitter this season, going 13-for-50 (.260). His three-run home run off Mets closer Billy Wagner in an 8-6 victory on July 8 was his biggest hit in a Padres uniform, though his contribution, even in a short time, extended far beyond mere statistics.
"He's a guy whose presence can be felt when he's in the room," Padres outfielder Jody Gerut said. "There are some iconic names out there where you're aware they are in the room. He's someone who makes you feel better about yourself, almost like a security blanket because of his experience and his ability to be a father figure.
"There's a value in someone who has won in the past and lost in the past and knows how to approach it mentally."
Clark figures to get more playing time at first base for Arizona as well as provide a left-handed bat off the bench. He'll also be counted on to provide leadership in a clubhouse that is considerably younger than San Diego's. He will also get a chance to sleep in his own bed in Peoria, and spend more time with his family.
Still, leaving the team he grew up rooting for and one he was excited to join in February wasn't easy.
"Obviously the goals that we set as a ballclub during Spring Training have not been met to this point, but I enjoyed my time there and being with the guys in the clubhouse," Clark said. "I'm just very thankful for the way I was treated by the fans in the short time that I was able to wear the San Diego uniform. They were great to me and I appreciate that."
Clark mentored some of the young players on the team, like Rule 5 pickup Callix Crabbe -- who was offered back to the Brewers in May along with other Padres.
"Tony made a lot of contributions. He was second in the league in pinch-hits, [and] got some clutch base hits along the way," Black said. "He was a big part of our club, on field and off. I think a lot of our younger players learned a lot from Tony. Hopefully those lessons will stay with guys."
Scribner, who turns 23 on Saturday, was selected in the 28th round of the 2007 First-Year Player Draft after four years at Central Connecticut State.
Scribner is 2-4 with a 1.64 ERA in two Minor League stops, including Class A Visalia. Over his first two professional seasons, Scribner is 3-5 with 11 saves while sporting a 2.27 ERA and 123 strikeouts along with 24 walks in 91 1/3 innings. He'll join Class A Lake Elsinore.
The Padres played Thursday's game against the Cardinals with 24 players, though right-handed pitcher Clay Hensley has been summoned from Triple-A Portland. He'll join the Padres on Friday when the roster move is officially announced.
Corey Brock is a reporter for MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.