The activated shortstop from the 10-day injured list while also optioning to Triple-A Indianapolis on Monday.
Kiner-Falefa was placed on the injured list on May 3, retroactive to May 1, with a right hamstring strain.
The infielder had reportedly resumed baseball activity and had been expected to run the bases over the weekend to test the hamstring.
The 30-year-old was hitting .280 with seven RBIs and six stolen bases prior to the injury.
Peguero, meanwhile, heads to Indianapolis after collecting two hits in nine at-bats across four games for Pittsburgh after being recalled on May 2.
