The loss, 9-6, to the D-backs now ranks as the longest Major League game this season. The Padres also hold the record for the second-longest game of the season: a May 16 win over the Reds after 16 innings at PETCO Park.
Trailing two games to one in a four-game series against the D-backs, the Padres were challenged to put the lengthy loss behind them to prepare for Monday's series finale.
"Hopefully, we won't do this anymore," catcher Henry Blanco said. "Every time we have to do extra innings, we're gonna do it. But let's not do it tonight."
The Padres are no strangers to recent extra-inning slugfests. The franchise's longest game in history took place April 17, 2008, in a 22-inning loss to Colorado at PETCO Park.
Padres closer Heath Bell expressed confidence in his team's ability to recover from the taxing loss, unlike the 22-inning defeat that many labeled as the downfall of last year's squad (63-99).
"It is tough to lose like this, but it's one of those things where we battled and battled," Bell said Sunday after the game. "If we keep our heads up tomorrow, it's not going to be that big of a deal. If we come out like gangbusters like I know we can, and we win tomorrow, I think we will have totally forgotten about this game.
"This isn't going to be like last year's 22-inning game and then us losing a million games."
Padres pinch-hitter David Eckstein sent Sunday's game into extra innings with a two-out, three-run homer in the ninth.
"I was only out there for one pitch, but the guys, they did a heck of job staying mentally tough out there," Eckstein said. "To do what they did, to go that long without making any mistakes ... it's tough to lose a game like that."
After Eckstein's ninth-inning heroics, Arizona relievers walked three and held the Padres hitless in extra innings.
"We didn't have any threats there after the ninth inning," Padres manager Bud Black said. "That's baseball, though. They pitched us well."
The Padres went through 10 pitchers in the loss, including shortstop Josh Wilson when the team ran out of options from the bullpen.
Padres pitcher Chad Gaudin, who started in Friday's loss, pitched the 16th and 17th innings. Gaudin said it was difficult to absorb the shock of losing such a long contest.
"I was like ... 'We played 18 innings and lost,'" he said. "We got outmanned I guess you say. We just ran out pitchers. You hate to lose a game like that, because you spend six-something hours devoted to one thing, and that's to win the game.
"When you come up short, it hurts a little bit more because it was almost taken out of your hands. That's a hard thing to eat."
Gaudin said he remains confident in his teammates' ability to prevent the disappointment from lingering in the clubhouse.
"What happened yesterday, happened yesterday," he said before Monday's game. "What happens today, happens today. We'll take it day by day."
Amy Brittain is an associate reporter with MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.