Stockton was introduced as a half-time substitute up front against Scunthorpe in place of Michael O'Halloran and scored the game's only goal which, along with Sheffield United's shock defeat at home to Hartlepool, sent Rovers back to the top of the table.
Captain James Wallace remains out with a medial knee ligament injury, while fellow midfielder Liam Palmer and top scorer Jake Cassidy are due to play the final games of their respective loan spells from Sheffield Wednesday and Wolves.
Tranmere boss Ronnie Moore is hoping to agree an extension for Bolton's O'Halloran, whose current spell expires after the FA Cup third-round tie against Derby, but Cassidy will return to Wolves as previously arranged and Palmer's situation is complicated by negotiations over a new contract at Hillsborough.
Moore told his club's official website: "We've spoken to Bolton about Michael, we're hoping we can extend his loan for a month. I'm just waiting on their manager (Dougie Freedman) to come back to me.
"Palms has been offered a new contract at Sheffield Wednesday and if he doesn't sign it they're going to take him back.
"He's due back after the Bury game but we're hoping we can speak to Dave Jones and get him to agree to let him come back here. We'll have to wait and see.
"Cass, we've just got to wait. But I won't wait too long and if I can get another striker in I will."