Pagan had missed all but one of San Francisco's previous seven games, prompting speculation that he could be sidelined.
"It's just time to get something done," Bochy said. "This thing's been nagging at him for three, four, five months, and it's not getting any better."
Pagan's impact on San Francisco's run production was undeniable. With him in the lineup, the Giants had a 56-35 record. Without him they were 29-36 entering Tuesday night's game against the Dodgers.
Pagan's 44-game midsummer absence with inflammation in his back was a primary reason for the Giants' slump after their record crested at 43-21 on June 8. After Pagan went on the disabled list on June 25, the Giants lost seven of their next eight games, absorbing shutout defeats in three of them and mustering two runs or fewer in three others during that span.
Pagan batted .300 in 96 games and ranked fourth on the club with 56 runs despite playing relatively seldom. He stole 16 bases, sharing the team lead in that category with Gregor Blanco, in 22 attempts.
The Giants endured similar troubles last season, when Pagan injured his left hamstring in late May and needed surgery, which sidelined him until Aug. 30. During that stretch the Giants dropped from a tie for first place in the National League West to a tie for fourth. They ultimately finished tied for third, with a 76-86 record.
The switch-hitting Pagan excelled in 2012, right before he was eligible for free agency, establishing personal bests with 95 runs, 38 doubles and 15 triples. That prompted the Giants to give him a four-year, $40 million contract.
Lacking Pagan, the Giants will continue to use Blanco as their primary leadoff batter and center fielder. Bochy named Juan Perez, Chris Dominguez, Gary Brown and Travis Ishikawa as candidates to fill the left-field vacancy through the rest of the season. Michael Morse, the Opening Night center fielder, remains bothered by a strained left oblique and has missed 18 of the last 19 games.
Bochy reacted stoically to Pagan's unavailability.
"You have to deal with these things. Injuries are, unfortunately, part of the game," Bochy said. "I think the important thing for us is to do what we normally do when this happens. You don't talk about it. You can't dwell on it. You just focus on what you need to do. It'd be nice to have him, but we don't."