Thorne were long-time leaders of the Premier North Division but surrendered top spot during the latter stages of the season.
They needed to beat Retford and hope that leaders Newark Town lost at Glapwell to take top spot.
Newark suffered a surprise 1-0 defeat in their final fixture – handing Thorne a golden chance to secure promotion to the Northern Counties East League.
But Colliery could not take advantage as they were well beaten by Retford, who as a result leapfrogged the hosts into second spot.
Thorne suffered an early blow when goalkeeper Dan Porteous went off injured after only 20 minutes.
Mark West (2), Aaron Fell and Liam Frost netted for Retford before Evan Fortune-West pulled one back in the last few minutes.
Harworth Colliery won 3-1 at Dinnington Town and finished sixth in the table.
Their three goals came from Liam Arnold, Cory Goodwin and Harry Dunbar within a seven-minute spell in the second half.
AFC Bentley came from two goals to win 3-2 against Askern Miners.
Quickfire goals from Neil Johnstone and Tom Speight had Askern in the box seat at the break.
But second half goals from Joel Tomlinson, Marcus Goodwin and Craig Aspinall completed Bentley’s comeback victory.