The Welshman was named in charge of the best 11 second tier players which didn’t include any from Kenilworth Road, although did have Fulham duo Aleksander Mitrovic and Harry Wilson, plus Bournemouth’s Dominic Solanke.
Jones took the honour above promoted duo Scott Parker and Marco Silva though, plus play-off rivals Steve Cooper and Carlos Corberan who have had fantastic seasons at Nottingham Forest and Huddersfield respectively.
When reflecting on what the club’s achievements this term mean on a personal level, Jones said: “Massive, it's been a real successful season for the football club and for myself personally.
"To have won the manager of the year award, this kind of backs it up a little bit because if I’d have won that and not got in the play-offs, some people might have said, ‘maybe someone else should have got it.’
"But with the lowest budget, as we are lowest budget in the league but in the top six, we’re dwarfed by everyone.
"So with the resources, what a wonderful achievement and I’m so proud, but it’s not just the manager.
"As I’ve said before, I've worked with a far bigger budget than this and didn't get anywhere near the results I've got.
"So it’s not the manager, you’re only as good as those that work with you and work around you, and this group are far, far, far better than the group I had in my previous club.”
Town sealed their place in the play-offs thanks to Harry Cornick’s moment of magic at the weekend, leaving Reading keeper Orjan Nyland with copious amounts of egg on his face to score the only goal of the game on the stroke of half time and secure the victory Luton needed to finish sixth.
In the end it mattered little as both Middlesbrough and Millwall, the only sides who could overtake the Hatters, lost their matches, although Jones hadn’t been paying too much attention to what was happening elsewhere, adding: “Not really, they (the players) didn’t know what was going on.
“I didn't want to know, but Kev Dearden said ‘do you want to know?’
"I said ‘unless it’s good news’ and he said, ‘well Preston are 4-1 up and Bournemouth are one up,’ so we knew it was a big shift needed.
“But I wasn’t concerned with that, we said win the game, win the game nothing happens, they could have won 100-0 and we’d have still been in the play-offs.
“So that’s all it was, yes, if we had to hang on, then it would have been a bit nervous, but they played six (minutes of stoppage time) and then added another one and played seven, so we never do it easy.
“But we should be in the play-offs anyway, as we scored a perfectly good goal against Blackpool, so it would have been a travesty if we hadn’t.
"As we have 100 per cent statistically, game-wise, everything, been one of the best six sides in the division this season, because all our numbers back up everything.”