The Frenchman beat Rickie Lambert and third-placed Jack Cork in the supporters' vote with an overwhelming 68.6 per cent approval.
Highly rated left-back Luke Shaw was overlooked for the Scholar of the Season award, with the honour going to midfielder James Ward-Prowse, while Jason Puncheon's stunning equaliser against Chelsea in January was named Goal of the Season.
|14/1||Morgan Schneiderlin is 14/1 with PaddyPower to score the first goal in Saints v Stoke City
"Thank you to all the fans," he added after securing the double. "I've been here five years and they've been brilliant. They always support us.
"There are many players in the squad who deserve this as well but I won't name names."
Manager Mauricio Pochettino, speaking without the aid of his interpreter, hailed Schneiderlin as a worthy winner.
"I must apologise – my English is not good! I believe Morgan deserves this trophy," he enthused. "For me, all the players, staff and supporters have done a great job in the last four months.
"I am very happy with the reception. Now your family is my family. Now it's time to enjoy this moment. After the last game, it's time to work for next season."