Jacobson, on loan at Rovers from Cardiff City, had resigned himself to missing the final but Rovers boss Paul Trollope (working under Director of Football Lennie Lawrence) made one last unsuccessful effort to get Joe's loan extended.
"We tried, but rules are rules and I don't think there's much sentiment when it comes to Football League rules," said Trollope.
"We're disappointed because Joe has made a big contribution to us.
"He's a young lad and I think that's sometimes forgotten by some people, but he's done well and has given us a natural balance and produced good performances.
"It is disappointing for Joe and the club, but he'll just have to sit and watch like he did at the Millennium Stadium."