Recalled duo Stuart Fleetwood and James Dance were replaced at the break and substitute Aaron O’Connor drilled home the decisive second half penalty.
Assistant manager Alan Neilson said: “We don’t want to be predictable and changed to 4-4-2.
“We created a few chances early on but didn’t take them.
“We came in at half time and had a chat with myself, Cards (Paul Carden) and the gaffer, and the gaffer decided to change it back to 4-3-3.
“Teams come here and they match us up. First half they matched us up 4-4-2 and second half we changed to 4-3-3 and they went exactly the same way.
“They were a team that played in the Football League last season and we had reports on them that implicates on Saturday they were unlucky.
“They showed they were well organised and very hard to break down.
“There is always pressure here when you play at Luton Town and teams will come here and match us up and put us under a lot of pressure.
“I thought we did well, got the goal and then we could relax a little bit.
“Kevin Pilkington pulled off a great save when it was 0-0 which was important as well.
“That’s why we work on the goalkeeper, the back four, the whole team as it’s a team game.”
Neilson asserted it wasn’t a reflection on the withdrawn players, saying: “It was just tactical. We spoke about it and changed.
“Fleets in training has been working really hard and knocking the goals in.
“We’ve got JP Kissock who could have come on as well.
“I don’t think we created enough, although we still had chances in the first half.
“They hit the crossbar with a great shot but we felt we needed a little more width and went back to a formation that suited us for the last five, six games.”
Neilson did have words of praise for substitutes Robbie Willmott and goalscorer O’Connor as he continued: “He scored two goals in the last two (home) games and was unlucky to be left out.
“We’ve got a squad here where we can pick 16, 17 players and they will all do a good job.
“We’ve got Robbie and Azza who are absolutely great players and great subs to have and they are pushing to get into the starting XI.”
Striker Danny Crow felt it was the change in formation that made the differences, saying: “They had men behind the ball and the fans and everyone was frustrated first half and then the gaffer changed the formation, a few personnel as well.
“I don’t know if the personnel did but the formation made a lot of difference.
“To win 1-0 is very nice but it could have been more, but it was a hard game and everyone was frustrated. These are the games you’ve got to win to catch the top two up.
“We think we are a very entertaining team so the 1-0s are frustrating for the fans but we’ll take that all day long.
“They are a good team and the gaffer said their league position doesn’t justify how well they’ve done.
“They are well organised and you heard it on the bench, stick to the gameplan. The gameplan was to try and frustrate us and get everyone behind the ball, but in the end it didn’t work.”
O’Connor admitted he was disappointed to start on the bench, but pleased he was able to help make a difference.
He said: “I’m always disappointed to be on the bench, especially when I felt I should have played but it’s just one of those things, get on with it.
“You are at a big club, with good players and the manager chose to change the formation and a few players today and maybe looked at them and thought we needed a little change-up with personnel and shape.
“We went with a 4-4-2 and a couple of changes but got it right in the and that’s the main thing and got the win.
“Players like myself and Robbie are similar types of players. Players that you would probably want to see coming off the bench at half time or second half when maybe defenders are getting tired.
“People with a bit of energy, especially Robbie, he’s got good tricks, good feet and good delivery and quickness so impact subs.
“To come on and score the winner was good but the win was the main thing tonight. To keep the run going, it was good to keep another clean sheet.
“I think that’s four clean sheets out of the last five and five wins on the trot so things are going well.
“A lot of clubs in this league and in football in general have a main man that’s head and shoulders above everyone else in terms of goals.
“But we’ve got a good number of players heading towards double figures so we are kind of evening it out.
“It’s healthy competition and everyone is happy for whoever scores and it’s good competition at the same time.
“We had to dig deep. I thought they came here, played well, had a gameplan, acquitted themselves really well.
“Had spells in the game where they had a few chances, but I thought overall we deserved the win.”
Town’s players and management still believe they can catch the top two of Fleetwood, who went top with a 4-1 defeat of Barrow and sit six points above the Hatters with a game in hand, and Wrexham, who are five points ahead with two games in hand.
Neilson said: “All we can do is worry about ourselves and keep on picking up the three points and the one points and keep on closing the gap at the top.
“We will worry about our three points each game and keep on putting the pressure on them.
And O’Connor added: “Teams will be looking down and looking at our form. We must be up there with the top two or three teams in the league in terms of form, and they must be looking and saying they are starting to come up now.
“I said about four, five weeks ago we haven’t hit a run yet. This is our first run. Other teams, Fleetwoods and Wrexhams have pretty much been on runs all year, they will hit a blip and hopefully when they do we will continue our run and we can catch them.
“Wrexham haven’t played today but we’ve got the three points on the board so it’s positive stuff.”