PHOENIX -- It's uncommon when a club trails for an entire game and still feels like it should have won.
But for the D-backs on Thursday, there was no doubt they knew they let one slip away.
And as the regular season winds down and the team's playoff hopes dwindle, there were no moral victories in the clubhouse for nearly completing a comeback from four runs down. The only feeling was defeat from a disheartening game that could have had a much different ending.
Working the bases loaded with nobody out in the ninth inning, the D-backs came up empty in their final three at-bats, falling to the Padres, 6-5, at Chase Field and snapping their three-game winning streak.
"You expect to at least tie the game up," D-backs manager Kirk Gibson said. "We had three opportunities, we were unable to do so. That part was disappointing."
With the defeat, Arizona fell to 5 1/2 games behind the Cardinals for the second National League Wild Card spot with 13 games remaining in the regular season.
After Chris Johnson led off the ninth with a single, Ryan Wheeler grounded to second base for what could have been a double-play ball. Fortunately for the D-backs, Logan Forsythe mishandled the grounder and Johnson beat the second baseman to the bag as everyone reached safely.
"I was a little too quick and overran the ball," Forsythe said. "But our bullpen came in and did a good job of picking us up."
Pinch-hitter Jason Kubel drew a full-count walk to load the bases with nobody out before Mike Jacobs popped out, Adam Eaton grounded out and Aaron Hill struck out to end the game.
Eaton attempted to lay down a squeeze bunt in his at-bat, but missed the ball entirely before hitting a grounder to second and having Johnson gunned down at home.
"I just missed it, I think it was a cutter away," Eaton said of the bunt. "But then most of the time with the infield in, you can get a ball through on a hard hit up the middle. That's what I was trying to do, it didn't work out."
The afternoon contest ended one batter before Justin Upton could come to the plate. The outfielder highlighted Arizona's offensive day, finishing just a home run shy of the cycle.
"It's rough," Upton said of watching the ninth. "I was pulling for every guy that went up there. We were inches away from getting the game done. It's rough, but we battled back, we didn't take the foot off the gas. That's all you can ask."
With his standout performance Thursday, Upton has seven extra-base hits in his last five games after totaling five in his previous 25 contests.
"I am seeing the ball well, I got some good fastballs to get, I was able to get the bat on it," Upton said. "It felt good. I've got good rhythm right now."
As disappointing as the day ended for the D-backs, it didn't start much better for the D-backs starter Tyler Skaggs, who made his sixth Major League start.
The Padres got to Skaggs early Thursday, tallying a quick three runs on a blast by Jesus Guzman to left field on a 0-2 pitch with two men on. In each of the 21-year-old's big league appearances, Skaggs has given up at least one home run.
"I wanted a fastball up, it wasn't as up as I wanted it to be, that's pretty much the moral of the story," Skaggs said. "I didn't think it affected me, I gave up another run, but I felt like I was fine. They are a scrappy team, they fight off a lot of pitches."
For Skaggs, Thursday was the rookie's third straight sub-par outing while struggling with command. The lefty lasted five innings, surrendering four earned runs on seven hits and three walks.
"He struggled, he threw a lot of balls," Gibson said. "He learned some things today. He's under a lot right now. It's part of it."
In his first three starts with the club, Skaggs allowed a combined five runs over 17 1/3 innings. But since then, he has given up 14 runs in just 12 innings of work. Two of the runs Skaggs allowed Thursday reached base via a walk.
"It's a learning experience, you have to make pressure pitches in pressure points," Skaggs said. "I've got to get ahead of batters. When you start falling behind, it's tough."
Down by three early, the D-backs battled back to cut the deficit to 4-2 with a solo home run from Hill and an RBI single from Johnson, but Brad Bergesen gave back both runs in the sixth to leave Arizona trailing by four.
After Paul Goldschmidt and Johnson each provided RBI hits in the sixth to get the D-backs to within two again, Eaton launched his first career home run to right field in the seventh to make it a one-run game and set up the ninth inning dramatics.
"It was good to get that out of the way," Eaton said of his homer. "I haven't gotten the ball back yet though."
Tyler Emerick is an associate reporter for MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.