Officers arrived at the man's home about 4:30 p.m. in the city of Hawk Point.
The man, who was not identified by police, was taken to a hospital. His condition was not immediately known.
The girl's family still wants to know where she was for 26 hours.
"Somebody knows what happened other than just the suspect," said St. Louis County Police Chief Timothy Fitch.
One minute she was playing in her front yard. The next, Maier was the focus of an Amber Alert.
Her brother with the barest of descriptions said Maier had been taken by a white man in a dark car with front-end damage.
And then, 26 hours later, she had been recovered 80 miles away from her Missouri home.
Someone called police to report seeing a little boy wandering around a car wash. It was Maier with her hair cut short.
"I mean, I still have the butterflies and I want to see her, so much," said Maier's aunt, Carrie Doyle.
Police credited the community's response for spreading word of Maier's disappearance quickly.
Volunteers fanned out to hand out flyers and support one another.
"This is a very tight-knit community," said Mike Kaste with the FBI. "Everybody knows each other, so what we're asking everybody is take stock. Did you see anybody? Anybody suspicious?"
On Thursday, Maier is back home with her family, who are still haunted by the thought of what might have been.
"I don't know, I just can't imagine her not being in our lives," Doyle said.
Maier's family said she appears to be okay.
She underwent several hours of tests at the hospital and then went home with her parents.