Falcons coach Mike Smith said Baker will have a discectomy, and he said the procedure will be performed in California, where he was examined by specialists on Wednesday.
A discectomy is the surgical removal of herniated disc material that presses on a nerve root or the spinal cord, according to WebMD.com.
"We really don't want to put a time frame in terms of how long before he returns," said Smith, who called the surgery "minor" when he announced plans for the procedure after Wednesday's practice.
"After the procedure, I think we'll have a better idea then."
Baker missed last week's game at Philadelphia with what was called a hip injury. When Baker did not respond to treatment, he was scheduled for appointments with two specialists.
The Falcons would not reveal details of the surgery or even say where the procedure will take place. Smith said the surgery will not be performed in Atlanta.
Baker, from Southern Cal, was the 21st overall pick in the first round. He was the Falcons' second first-round pick, following quarterback Matt Ryan, the No. 3 overall selection.
Baker has started five games at left tackle. He missed the Sept. 28 game at Carolina with a concussion after leaving two games earlier in the month with head injuries.
Todd Weiner, who started for Baker at Philadelphia last week, was held out of Wednesday's practice with a sore knee.
The Falcons signed veteran free agent Wayne Gandy. The 37-year-old Gandy started for the Falcons in 2006 and 2007, when his season ended with a knee injury in Week 5 at Tennessee.
Smith said Weiner would start at left tackle in Sunday's game at Oakland.
Weiner seemed less confident.
"I think right now it's day to day," Weiner said. "I'll see if I can get a little better each day and get myself ready for Sunday."