The defender joined the Championship side in the summer with a view to spending the 2015/16 campaign at the Riverside.
The 21 year-old made just five appearances during his time at the club, four of which came in the Capital One Cup.
Stephens did play his part in a memorable win for Boro back in October as they beat Manchester United on penalties at Old Trafford, but his chances were still limited after that.
The defender has now returned to St Mary’s and is available for Saturday’s Emirates FA Cup clash with Crystal Palace.
On Stephens' return, Saints boss Ronald Koeman said: "Jack is back from Middlesbrough. He wasn't playing there and then why is he on loan if he doesn't play? It's better for him to come back."