Two quickfire goals from Danny Hylton and Luke Berry just after the hour mark put the Hatters in a strong position, but a Johnny Mullins own goal in the 81st minute setup a tense ending as the hosts went in search of a late equaliser, although their efforts were thwarted by a tight Town defence.
Jones said: "After the own goal it lifted their spirits slightly and they threw everything at us. We had to defend that out, but we should have been out of sight by then, we had enough chances.
"I am very, very pleased though. It's topped a wonderful week off – nine points, we remain top of the league, three different victories and performances, but I am so pleased.
"To be fair I thought we had the play first half. I think we won the game in the first half. It was horrific down there, it was blowing a gale and we were playing against it in the first half. So to carve out the amount of chances we did – not clear cut chances, we had a few, but with a little bit more quality we would have taken the lead.
"I thought we defended excellently, I thought we defended set plays well and the game was won. We just had to get out of the traps and get that first goal.
"We started the second half well, but they changed for us. They played a back five, then a diamond, then one up front – which shows the kind of respect they showed to us.
"But then when they changed I felt the space was opening up. We made a little change and went back to the diamond and I thought Andrew Shinnie coming on changed the game.
"We really showed quality, we scored one and then two straight away, and we could have had more, especially on the counter. Shinnie had a great chance after great hold up by Danny. But I am really pleased, I would have taken 2-1 any day of the week."