Machado was hit by a pitch that fractured the metacarpal in his left hand on May 15. The third baseman struck out twice and hit into a fielder's choice and lined out in his other two at-bats.
"Every day, it has been getting better," Machado said before the game. "It's getting to this point that it's not even hurting anymore. So, it's about that time to get back in there and play some games."
In 41 games, Machado is hitting .231 with five home runs and 19 RBI. He has only 12 extra-base hits and nine groundball double plays.
In other moves, San Diego placed designated hitter Nelson Cruz on the 10-day IL with a strained right hamstring and optioned outfielder José Azocar to Triple-A El Paso.
The Padres also selected the contract of first baseman Alfonso Rivas from El Paso.
To open a spot on the 40-man roster for Rivas, catcher Luis Campusano (left thumb surgery) was moved from the 10-day IL to the 60-day IL.
The Associated Press contributed to this report.