The former England U-21 international made just 20 appearances for the Saints last season after first suffering a broken metatarsal and then a bad ankle injury in the FA Cup clash at Leicester at the end of January.
Kevin Blackwell is still hoping to strengthen his midfield after losing new signing Kevin Nicholls for three months due to a training injury and selling David Livermore to Hull after less than two weeks at Leeds following his move from Millwall.
Stoke City were also hoping to sign Prutton but claim they have been gazumped at the 11th-hour by Leeds.