The D-backs have dropped four in a row and are 3-10 since Gibson took over for A.J. Hinch on July 1.
It may not have been enough, but the D-backs did show some fight, literally, against a San Diego team that has beaten them six straight times.
The benches cleared in the sixth inning when Arizona third baseman Mark Reynolds and Evereth Cabrera got tangled up on a pickoff play at third. Cabrera was tagged out on the play, Reynolds fell on top of him and Cabrera kicked Reynolds, which prompted him to take a swipe at Cabrera. Reynolds missed and Cabrera was ejected.
"He was too far off the bag and [catcher Miguel Montero] threw it, and the only play I had was to lunge at him," Reynolds said. "We got tangled up and he kicked me kind of in the stomach with his foot. I had to defend myself. That was really it."
The D-backs grabbed a quick lead when Chris Young led off the game with a single to left and Kelly Johnson followed with a home run to right.
The Padres, though, chipped away, scoring single runs in each of the second, third and fourth innings against starter Edwin Jackson to take a 3-2 lead.
The D-backs tied up the game in the fifth on a homer by Justin Upton, but the Padres retook the lead in the sixth when Cabrera tripled home Chris Denorfia.
The Padres tacked on a pair of insurance runs in the eighth, but the inning could have been worse.
In fact, after Reynolds threw wildly to first on a bunt by Tony Gwynn, which allowed the second run of the inning to score, Gibson jogged to the mound and signaled the entire infield to join him.
"Let's stop it right here, let's slow down, think about what we've got at hand, let's get out of here three down and give ourselves a chance," Gibson said of what he told them. "The tendency is things snowball, boom, boom, boom and they get out of control."
The D-backs were able to get out of the inning without further damage and they staged a furious rally against closer Heath Bell in the ninth.
The rally started with two outs and two strikes on Young, who managed to extend the at-bat to eight pitches and draw a walk. A single by Johnson and an RBI double by Justin Upton put runners on second and third and brought the potential go-ahead run to the plate.
Bell, though, got Montero to ground out to end the game.
Had they been able to pull out the victory, Gibson thought it could have gotten them on a roll.
"The frustrating thing from where I sit is if we can come back and win that game, it's just what we need," he said. "I'm happy with the effort, but we can't keep saying, 'Ah, we played good.' We should compete every day like that."
Reynolds said that is what he and his teammates plan on providing the rest of the way.
"No one is more frustrated than the players in this clubhouse or the coaching staff," he said. "It's tough sledding, but they're not going to cancel the rest of the season so we're going to go out and play and keep competing and try to win some games."