Aoki, the Giants' primary leadoff hitter, rejoined the lineup Monday night batting in the eighth spot for the first time this season.
"We're doing pretty good right now," manager Bruce Bochy said. "I don't want to break up what's going on with the batting order. ... This will give [Aoki] a chance to get settled in and not run quite as much."
Prior to taking a Carlos Frias fastball off his right leg June 20, Aoki was hitting .317 with two home runs, 33 runs scored and 19 RBIs in 67 games.
Arias has been one of the Giants' main utility players since the team signed him to a Minor League contract in December 2011. He was on San Francisco's last two World Series championship teams, but hit .207 with one home run and four RBIs in 40 games this season.
"Very difficult decision," Bochy said. "Joaquin's been part of us through our success and spent a lot of time here and has done a real nice job for us."
Bochy added that part of the reason the team designated Arias is because it did not want to lose the youth that infielder Ehire Adrianza provides on the bench.
"He's probably our best shortstop besides [Brandon] Crawford," Bochy said. "We really didn't want to take a chance on losing him. At his age, we think he has a chance to be a nice utility player."
The Giants had Aoki and Hunter Pence in the lineup together Monday for just the 14th time this year, and they are 9-5 in those contests.
Despite not being at full strength on offense for much of the season, the Giants entered Monday first in the National League with a .274 batting average and .330 on-base percentage, and second with 426 runs scored.
• Giants catcher Andrew Susac, who is on the 15-day disabled list with a sprained right thumb, said Monday he is scheduled to resume throwing Tuesday. He remains on schedule to return to the team when eligible Aug. 3.