Johnson’s first-half strike gave Old Boys a 1-0 lead at home to Grimsby Borough Development A and then struck after the break to seal a narrow 2-1 win which moved them up to fifth.
Old Boys have now lost one of their last four.
Louth Town Reserves stayed bottom of Division One, but picked up a positive result at home to Immingham Town Reserves.
The sides fought out a goalless draw at London Road.
Alford Town staged a second half comeback at home to Scamblesby to go top of Division Two.
With leaders Manby involved in cup action, Alford were looking to replace them at the summit, but trailed 1-0 at half-time.
But Joe Irving struck twice after the break and Jess Barrett was also on target to complete a 3-1 win.
Town now lead Manby on goal difference and with two games in hand.
Sutton Rovers went crashing out of the Town Trophy after surrendering a two-goal lead from their first leg against GB Kitchens.
Rovers went into the second leg of the quarter-final tie with a 4-2 lead, but the Division Three leaders took the match 4-0 to complete a 6-4 aggregate win.
In Division Three, bottom side Alford Town Reserves had an afternoon to forget at home to Burgh Athletic.
Paul Skipper hit a hat-trick, Joba Harness and Lance Simons both scored twice, and Mitchell Wynn also found the net for the visitors in an 8-0 win.
Selected fixtures –
Tom Sandys Trophy final, 7pm: Alford Town Res v Louth Old Boys Reds (at Bradley Development Football Ground).
Division One, 2pm: Louth Town Res v Louth Old Boys.
Division Three, 2pm: Louth Old Boys Vets v AFC Grainthorpe.
Junior Challenge Cup quarter-final first legs: Alford Town v North Somercotes United; Sutton Rovers v Marsh Rovers