The A's rallied for three runs off All-Star closer Jonathan Papelbon to tie the game, and that momentum carried over into the 11th, with two runs that led their triumph.
In his third year on the coaching staff but his first as Geren's bench coach, Waller, who has one year of Minor League managing experience and was the Padres' director of player development from 2000-05, did his best to downplay his role in the victory.
"I ended up taking over the car, but what happened was because of the players," Waller said before the third game of a four-game series at Fenway Park. "A lot of good things happened in the game, but relying on guys to make good judgments was the key."
Several players went in the opposite direction, praising Waller's poise and late-game leadership. Geren, too, joined the chorus.
"He did a good job," Geren said. "He stayed aggressive, made the right moves ... I'm happy for him."
Waller's most significant move might have been his decision to have Rajai Davis pinch-hit for starting left fielder Eric Patterson in the eighth inning, then letting Davis hit for himself in the ninth and 11th innings.
Available in all three instances was Bobby Crosby, whose nine-game hitting streak had been snapped Monday. Crosby was batting .310 over his past 15 games.
"Rajai was my last outfielder, and I liked the defense with Rajai in there," said Waller, who didn't have Scott Hairston as his disposal because of a strained left quad that prevented him from starting Wednesday, too. "I was saving Crosby for a situation where I needed an infielder."
Davis' infield single in the ninth tied the game, and after breaking the tie with a single in the 11th, he stole second base and scored the eventual game-winner on a single by Adam Kennedy.
Waller also let Nomar Garciaparra, who had doubled in the 10th, run for himself despite a chronic calf condition that makes every sprint a potential disaster.
Garciaparra, however, had looked fine while trying to beat out a double-play ball earlier in the game, and he stole third base with two out in the 10th before Jason Bay prevented him from scoring the go-ahead run by diving to snag a sinking line drive to left by Kurt Suzuki.
Said Waller: "[Third-base coach Mike] Gallego talked to Nomar and said he was fine, so I left him in there."
"Just a little reminder," Garciaparra said of his theft. "I do have my good days."
Geren said Waller has grown nicely into his role, saying he's leaned on his bench coach more and more as the season's gone on.
"He has a pretty good idea of what I want now," Geren said.
All Waller wants is to help the A's win games, and without question, he did that Tuesday -- with plenty of help, not only from his players but from his colleagues on the coaching staff, who handled the final seven innings as something of a manager-by-committee.
"So many people were involved with that win," Waller said, "that everyone went home happy."