Bowen is now being held at the Lawrence County Jail in Tennessee on $100,000 bond.
The Tennessee Bureau of Investigation put Porter on its Top 10 Most Wanted list last week.
While he was on the run, Porter's mother Barbara Wright issued a message to her son through the news station WKRN: '"on please bring yourself in. I love you so much son, I don't want you to get hurt. I don't want nothing to happen to you.
"Do the right thing, you know you didn't do this, please bring yourself in, prove to them you are innocent."
On Sunday, TBI officials tweeted that police in Scottsboro, Alabama, received a tip about Porter and found him walking alongside a highway, the Daily Mail reports.
He was taken into custody and extradited back to Tennessee. The 33-year-old is facing aggravated child rape charges.
Porter is now being held in the Lawrence County Jail in an isolation cell, for his own protection, on $1million bond.
According to an arrest affidavit, Porter and Bowen's son suffered potentially permanent damage after being sexually penetrated during the attack, reported WTVF.
The 16-month-old also sustained bone fractures from being held down during the rape.
The toddler underwent multiple surgeries and was later discharged from the hospital to continue his recovery in an undisclosed location.
Officials say neither Porter nor Bowen had legal custody of the boy. The couple also have a young daughter together.
Records cited by WHNT indicate that Porter has a criminal history, including a 2010 arrest on a charge of domestic assault.