Scales had been optioned to Triple-A Iowa on Wednesday to make room for infielder Andres Blanco, because the Cubs wanted someone who could back up at shortstop with Aaron Miles going on the disabled list.
"I never left," said Scales, who spent most of Wednesday getting treatment for the flu.
Freel was injured in the fourth inning of Wednesday's game after he had singled.
"I felt something about three quarters of the way down [the line]," Freel said. "I was definitely going to go for two. I felt something kind of twinge a little bit, nothing really major. I've had some hamstring issues."
Freel said he would need about five or six days, but he understood why the team placed him on the disabled list.
"In this situation, for the benefit of the team, it's a good idea to not sit there and be a man down, especially in the National League," Freel said. "I think this is for the betterment of the team. It's not something I want to go through.
"Nobody feels worse about it than I do. I cried like a little baby yesterday. I've been really upset. What can you do?"
The Cubs did get good news regarding pitcher Rich Harden, who has been on the disabled list since May 18 with a low back strain. Harden was able to play catch on Thursday.
"It's encouraging," Cubs manager Lou Piniella said of Harden's progress. "He didn't feel it, didn't feel a thing. Now we'll get him on a program to get him back on the mound. This was the first test, and he passed it with flying colors, which is the best possible news for us."
Carrie Muskat is a reporter for MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.