The Lilywhites manager’s team selection caused some raised eyebrows pre-match but turned out to be spot on.
Louis Moult came in for his first start since December 22, with Daniel Johnson chosen ahead of Alan Browne in the No.10 role behind him.
Both could have left PNE in the transfer window had things worked out differently but they produced the goods in the 3-0 win.
Sean Maguire, moved out to the left wing in order to bring in Moult, headed North End in front early on.
Preston North End's predicted line-up for Championship visit of Rotherham United
Preston-born Clarets legend Lenny Johnrose dies at 52
John Smith's PNE Fans' Panel verdict: Sunshine all the way
Luton Town boss says best team didn't win after Championship defeat to Preston North End
Preston North End showed the hallmarks of a successful side as they beat Luton Town
Moult scored the second and Paul Gallagher’s sublime goal clinched the victory.
Neil said: “I thought DJ in the first half was excellent. In the second half he didn’t get as high up the pitch and so his influence dipped just a little.
“It is always difficult when you replace someone like Alan Browne who has scored a lot of goals in the last two years.
“I just felt that at home, that little bit of creative spark hadn’t been there.
“So I did something quite bold, made four changes and dropped guys who had done very well for me.
“At the end of the day if I think it is the right thing to do, I will do that.
“Those type of calls don’t faze me at all.
“Louis Moult came into the team after not featuring at Millwall last week, that was a different kind of game.
“Sometimes you need to do different things for different games.”
Ball retention was key to this victory in Neil’s eyes, as was a slight change in how he asked his full-backs to play.
“Both full-backs were more advanced than normal,” said Neil. “We then had to make sure we retained the ball in the middle area and let them work up the pitch.
“If you keep giving the ball away you will get countered down the flanks.
“Wigan did counter us two or three times down the flanks in the first half when we gave the ball away cheaply.
“We tightened up and I was always confident we would win the game if we retained the ball well.”
Neil will rotate the squad for tomorrow night’s visit to Bradford City in the League Cup.
He won’t risk Fisher and Gallagher who were subbed in the second half.
“Both were precautionary measures,” said Neil.
“Gally’s Achilles tightened a bit and Darnell has done magnificently well to go from an operation four weeks ago to playing now.”
PNE will monitor Andrew Hughes’ fitness over the next few days, with the left-back holding his hamstring at the final whistle.