Nunez went 0-for-4 from the No. 9 spot in Minnesota's 7-2 win over Toronto.
It gave regular shortstop Eduardo Escobar a rare day of rest, as it was the first time he didn't start at shortstop since May 21.
"We're just moving them around," Gardenhire said. "He's played every day, and I wanted to see Nunez in there. He's been swinging the bat good, too. I like Nunez."
Rhett Bollinger is a reporter for MLB.com. Read his blog, Bollinger Beat, and follow him on Twitter @RhettBollinger. This story was not subject to the approval of Major League Baseball or its clubs.