The former Manchester United and Leeds United man had joined the Shrimps on a one-year deal last August.
He was one of 19 signings in three-and-a-half months as manager Stephen Robinson sought to build a squad capable of surviving in League One.
However, the 30-year-old failed to establish himself as a regular starter despite Morecambe having conceded the most goals in the third tier this season.
He made 14 appearances across all competitions, scoring once when the Shrimps defeated Lincoln City at the end of September.
It’s been rumoured that Wootton may now be embarking upon a move overseas.
Robinson said: “Scott leaves with our thanks for all his efforts during his time at the club and our best wishes for what promises to be a life-changing move for him and his family.”
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