The team announced it will place Aoki on the 15-day disabled list Wednesday, retroactive to Sunday.
Bochy penciled Aoki into Tuesday's lineup to play left field and hit leadoff, but scratched him after the outfielder felt some discomfort while warming up before taking batting practice.
"It was the type of pain I knew I couldn't play with," Aoki said through translator Kosuke Inaji.
Aoki, who suffered the injury Saturday after taking a pitch off the leg from the Dodgers' Carlos Frias, ran sprints early Tuesday afternoon with no pain, but when he tried to turn on his foot to swing, he noticed some pain in his lower leg. He was sent for another X-ray, which revealed the break.
"I was definitely surprised," Aoki said. "I came here ready to play. It was really weird that it got worse from that point."
With Aoki going down, the Giants catch a bad break at the wrong time. Bochy's ballclub is already without starting right fielder Hunter Pence and has struggled to score runs at AT&T Park this season.
"That's a blow for us," Bochy said. "That's a loss. You hate to see it happen to him."
Gregor Blanco, who went 2-for-3 with an RBI on Tuesday, looks to have fully recovered from his concussion symptoms and is the top candidate to replace Aoki. Blanco and Justin Maxwell appear to be the Giants' starting corner outfielders for the next few weeks.
With Aoki headed to the DL, the Giants figure to recall Jarrett Parker from Triple-A Sacramento to add some depth in the outfield. San Francisco will need significant contributions from Blanco, Maxwell and Parker to replace Aoki, who leads the team in hits and is fourth among NL outfielders in the latest update of All-Star voting.
"We've got confidence in everybody," Madison Bumgarner said. "It's certainly a hit, for sure, the way he's been playing. If we want to be the ballclub we want to be, somebody's going to have to step up."
• Right-handed relief pitcher Sergio Romo left Tuesday's game with a hyperextended left knee and Bochy said he is considered day to day. Romo retired the second batter in the ninth inning and limped in front of the mound before team athletic trainer Dave Groeschner came to check on him.
"He's done that before," Bochy said. "[Romo] was throwing good, but I could see him limping around."