An injury-time winner from Lewis Temple gave the B Team victory in their final home game of the season in the Central League.
The defender powered home a header from a 93rd-minute corner as the Whites finally found a way through.
Bottom club Chesterfield never made life easy as their young side defended well and also had a couple of chances of their own to grab the lead on the break in the second half.
But the Whites’ pressure paid off when Temple – who has done consistently done well for the B Team while waiting for his first-team chance – met a delivery from Jack Mawditt to nod home and secure the points.
Andy Taylor’s side had needed to work hard to gain the win which lifted them to third place in the table.
The Whites – who had John McAtee in their starting line-up as the forward waits to complete his three-match first-team ban – dominated possession but threatened only once before the break as Toby Ritchie sent an early chance wide.
Ritchie, fresh from an EFL debut as a substitute at Cardiff last Saturday, then nodded just wide minutes after the break and went even closer to breaking the deadlock with a shot which skimmed the top of the crossbar.
Chesterfield’s Chris Kondolo had a chance to punish the Whites but couldn’t apply the finish and after Temple had ended the stalemate there was one further scare for Wanderers as Luke Lomax was forced to save well from Marcus McKernan even deeper into stoppage time.
“It’s always nice to win but it was a strange game really,” said B Team boss Taylor. “It was an attack versus defence really and I understand why they did that.
“They were very young and we were much older, so it was a difficult one but it was a good one in terms of managing frustration, staying patient. It was just a case of us not getting frustrated, probing, probing, probing. They were just sat in a deep block and sometimes that’s difficult to break down.
“We had to be aware of the counter-threat because at times they did look a bit of a threat but we managed that quite well and in the end we got the goal from a set-piece. Sometimes when it's tight and teams are camped in their box, it is a set-piece that opens teams up, so fair play to Lewis and we were pleased to see that go in.”
Wanderers complete their league campaign at Derby County next Tuesday and are still awaiting a date for their scheduled Lancashire FA Senior Cup semi-final against Blackburn Rovers.
Wanderers: Lomax, Smith, Temple, Taylor (Trialist 70), Oliver (Grayson 80), Irwin, Sharples-Ahmed, Ritchie (Leigh 60), McAtee (Kirkpatrick 60), Lewis (Mawditt 60), Lawrence.
Chesterfield: Rinaldo, Yates, Wainman, Burton, Short, Grumley, Chambers, McKernan, Nkhonjera, Kondolo, Wozniczka. Substitutes used: Ellix, Shone, Nicholson, Reece.