The visitors took the lead after James Shea upended Andre Blackman in the penalty area, with Jack Taylor slotting away the resulting spot-kick just after the hour mark. The Hatters immediately responded through Elliot Lee, who curled the ball past Craig Ross and inside the far post.
With the score level at full-time, the game went onto penalties, with the Hatters winning 4-3 and earning themselves an extra point – which means they will qualify for the knock-out stages of the competition should they avoid defeat at AFC Wimbledon at the end of the month.
Jones said: "I thought it was a lacklustre performance to be honest in terms of there's a few out there who needed minutes, who needed game time, and it showed. I thought we were very lacklustre.
"We never looked like we were going to lose the game especially in the first half, but in terms of our overall performance we were very lacklustre. The keeper pulled off four fantastic saves – we had enough chances to have won the game.
"But credit to Barnet, it was a good, entertaining game – quite an open game. But as far as I am concerned we were off it. There were a couple of ones who were just coming back into it, needed the game time and that kind of showed I think.
"It was a competitive game, Barnet made a few changes as well. We know Barnet are a dangerous side, we saw that earlier on in the season.
"It did serve its purpose, Lawson D'Ath coming back from injury, Luke Berry and Pelly-Ruddock Mpanzu had important game time. Johnny Mullins and Aaron Jarvis got starts. Elliot Lee looked very lively to be fair to him, so did Jordan Cook.
"All of them had real good game time and it was a good run out, but we looked a little bit rusty if I am honest."