The 25-year-old spent two months of this season on loan with the Layer Road outfit and he looked to have sealed a permanent move to the Essex club at the end of October.
However, a last-minute hitch over a sell-on clause initially caused the deal to fall through and Stockley was forced to return to Oxford.
But further negotiations between both clubs has rescued the deal and the defender has signed a new 18-month contract with Steve Whitton's side, with the defender eligible to play against Bristol City on Saturday.
Stockley told The U's official website: "It has been incredibly hard this week, and it wasn't helped by the fact that no one at Oxford was telling me anything that was going on.
"I've been kept up to date by (Colchester chief executive) Marie Partner and Steve Whitton and I know that I've been a bother!
"Marie has been absolutely brilliant and I want to thank her for working wonders to get this deal sorted."
Meanwhile, Cameroon international striker Mvondo Atangana has signed weekly terms with the Division Two side after joining the club last month on trial.
The short-term deal could be extended if he continues to impress Whitton with his displays for the Layer Road side.
In other news, The U's denied local reports that youngster Lloyd Opara had signed for Cambridge United after impressing the Abbey Stadium outfit while on a month's 'work experience'.
The 18-year-old's displays have prompted Cambridge to ask Colchester about taking over the remainder of his YTS scholarship but no release forms have been signed by Opara at Layer Road.
Finally, former Colchester striker Triston Chambers has been handed a trial with Conference side Dagenham & Redbridge.
The 19-year-old hit-man was released last month by The U's for a breach of club rules and has been on the lookout for a new team ever since.
