The Rams recorded their second victory over the Latics in the space of just two weeks with forgotten man Junior striking the winner with just 11 minutes remaining.
But it was the omission of a number of key Wigan players that proved to be the major talking point as their manager Paul Jewell stressed the relative importance of promotion to the Premiership over possible cup glory.
The gamble appeared to be on the brink of paying off as the visitors dominated the first half and deservedly took the lead on 30 minutes. David Graham teed up Alan Mahon whose rising left-foot drive from the edge of the area gave keeper Lee Camp no chance.
Camp had just 60 seconds earlier made a remarkable stop to deny a Jason Roberts header as the Derby defence once again looked edgy in front of their home fans.
Roberts passed up another scoring opportunity minutes later as he dragged the shot across goal when well placed and Camp had to be at his best to repel a header from Mike Flynn just before the break.
A spot of reorganisation by George Burley reinvigorated the home side's approach, but it was not until the introduction of Junior in the 68th minute that the match turned on its head.
First Spanish midfielder Inigo Idiakez curled a spectacular 25-yard free-kick past keeper John Filan after striker Tommy Smith had been fouled.
The goal sparked a furious spell of end to end action with first Wigan pressing then Junior bearing down on goal only to see Filan block his shot.
The Rams took the lead on 79 minutes when Tom Huddlestone sent Smith through and the striker rounded the keeper and showed great composure to pick out his strike partner in a congested six-yard box.
There was one final act however as Wigan pressed for a replay, substitute Jimmy Bullard must have thought he had saved the tie when he met a cross from Gary Teale, but his goalbound header was miraculously turned over the bar by the highly-rated Camp.