Gibson was ejected for the second time in four days and watched, from his office, as Arizona lost to the San Francisco Giants 3-2 in 11 innings Sunday.
The Diamondbacks had a chance to go ahead in the 10th when Willie Bloomquist doubled with one out and, following the second out, Paul Goldschmidt was intentionally walked.
Aaron Hill, who entered the game with a .333 average over the previous six weeks, hit a grounder to Buster Posey at first base. Posey bobbled the ball, but recovered in time to deliver an underhanded toss to pitcher George Kontos, who had trouble finding first base and double-stepped.
First base umpire Tom Hallion, who tossed Gibson on Thursday for arguing a call at home, originally called Hill safe.
Giants manager Bruce Bochy asked if Hallion could get help on the play. Hallion obliged, talking with the rest of the crew before reversing his call and ending the inning.
"I just wanted to question the call," Gibson said. "He didn't want to hear about it, so I got thrown out."
Wade Miley, who could not get out of the second inning of his last start for Arizona, had made it clear the days between would be tough.
"You want to get back out as soon as possible," said Miley, who pitched seven solid innings. "But you can't worry about the last time out, you just go out and compete, give ourselves a chance to win.
Miley was lifted for pinch-hitter Eric Chavez, who hit a sacrifice fly to help the Diamondbacks tie the game at 2 in the eighth. A.J. Pollack also singled home a run.
"We have not swung the bats very well at all, especially in the good situations," Gibson said. "We're not in a good streak right now."
Angel Pagan hit a winning single in the 11th off Joe Thatcher (3-2) after Hector Sanchez singled and Gregor Blanco reached safely on a sacrifice bunt. Pinch-runner Ehire Adrianza beat the throw home.
Javier Lopez (3-2) got the win.
"You know it's going to be a close game," Miley said. "So you want to put up zeros, and then you want to hold it at 2-0 to give your team a chance."
Miley allowed two runs on five hits. He walked two and struck out three.
"I felt like I was struggling," he said. "But I was getting outs."
Matt Davidson walked to lead off the ninth for the Diamondbacks but pinch-runner Tony Campana was caught stealing. Miguel Montero followed with a single but was stranded.
Pollack doubled with one out in the first, the farthest any Diamondback advanced against Madison Bumgarner, who proceeded to strike out five in a row. He set down 10 of his final 11 batters.
NOTES: The Diamondbacks will start RHP Randall Delgado (4-5, 3.69) in their series opener against the Dodgers in Los Angeles on Monday. He's allowed three earned runs or less in 12 of his 15 career starts. ... Arizona INF Martin Prado missed his second straight start with an illness. ... Diamondbacks INF Cliff Pennington returned to Arizona after the game to be with his wife, who will undergo induced labor on Monday. ... Bloomquist is hitting .517 (15 for 29) in nine games since returning from the disabled list. ... Arizona lost its first extra-inning game on a travel day after winning its first 10. The Diamondbacks are tied for the major league lead with the Chicago White Sox with 22 extra-inning games.