Tykes substitute Aapo Halme netted shortly after coming off the bench to cancel out Luke Berry's first-half goal, but the point did little for either side's hopes of survival with just four games remaining.
Luton remain rooted to the foot of the table, while Barnsley are one point better off on 42, three adrift of safety with four games left.
Jones said: "I'm disappointed because of the lateness of their goal and how it came about, because I couldn't see them scoring.
"You always fear the worst as a manager but I couldn't see them scoring, I really couldn't.
"First half we gave them a little bit too much space and we didn't get close enough to them to meet balls in our box, but in the second half I thought we were excellent.
"Tactically we were really good, it's just late on, it came from a corner, that's the really frustrating thing.
"And then having the best chance of the game straight after to win it, you're just frustrated then.
"You want to hold out and make sure you win the game, I thought we were a lot better in the second half and just disappointed that we didn't hold out."
After Berry had fired Luton in front in the 14th minute, picking out the top corner with his left foot once Elliot Lee's effort had hit a post, Barnsley took over, with home keeper Simon Sluga denying Jacob Brown, plus Cauley Woodrow twice – the second a superb save, clawing away his looping header.
Luton improved after the break, with Berry dragging wide from the edge of the box after good work by James Collins, but substitute Halme popped up to level in the 84th minute.
Luton then should have won it moments later, their own replacement Harry Cornick going clean through on goal only to be denied by Jack Walton.
Tykes boss Gerhard Struber said: "I told my boys in the dressing room, we have to fight until the last game.
"We have to pick up points, today our big goal was three points, but we got one point and our next game is a difficult opposition, but if we have this performance, we can do it.
"I think the boys showed me, we never gave up, we had very good energy from everyone.
"The first half was completely in our hands and this is the right mood in this situation, never give up, fight until the last game.
"Today we're disappointed that we didn't use the best chances for us, but still it's one point."