Dan Potts' clearance found the back of his own net after it deflected in off Johnny Mullins midway through the first half, before Tom Pope netted on the hour mark to double the home side's advantage.
Ben Whitfield then added the third from Pope's pass before Vale's top scorer this season made it 4-0 with a close range finish eight minutes from time.
Results elsewhere see the Hatters remain top of the table and four points clear of second placed Notts County.
Jones said: "We were poor. We were second best from start to finish. We had a spell in the second half for about six or seven minutes that we looked like the team we are, and then apart from that we were second best.
"Apart from the first goal, the goals are horrific in terms of defending. But look, we didn't deserve anything from the game. I could come here and say the pitch was awful, there were three errors and [if we hadn't conceded those] then we could have got something from the game. We wouldn't have.
"They were better than us all over the pitch, won the second balls, they outworked us, they outcompeted us. We didn't handle Pope all afternoon and we got what we deserved.
"I freshened up the team because we've got four games in a week, and it's a big ask. So that might have upset the equilibrium. The pitch is awful here, it's really difficult to get any sort of football going, we knew that, but we just didn't defend well.
"They outfought us, they outbattled us, they worked harder than us. They were more dangerous than us, Pope was more of a threat than anyone else on the pitch, and they thoroughly deserved to win the game.
"I can't stand here and defend my team. We haven't lost in three months, we've got a game now to react quickly, but we were nowhere near today, absolutely nowhere near."