The Hatters went down 2-1 at Kenilworth Road thanks to Patrick Bamford's 90th minute winner, his second goal of the game.His first, seven minutes into the second half, followed a stirring Ben White run upfield after referee John Brooks ignored Izzy Brown's appeal for a free-kick.
Jones was aggrieved at that decision, felt Stuart Dallas had committed a foul in the penalty area that went unnoticed in the first half and did not believe Matty Pearson was offside when he put the ball in the Leeds net shortly after Luton had made it 1-1.
The Luton boss insisted he wasn't putting the blame on 'outstanding' referee Brooks but admitted those three calls were hard to take.
"I was delighted with aspects of the performance apart from the final result," he said.
"I think there comes a point where you have to admire the boys who give absolutely everything. They were four minutes short of getting a result.
"These are the best team, we nullified them today. I see them cutting through teams. They had more shots, more possession but we were always in the game. That's satisfying.
"I don't think I'm a biased manager, I try to be subjective with things. I've looked at the clips and it's a foul on Izzy, taking his leg away from him. It's a penalty on James Collins and in my opinion Pearson is onside. We're playing Leeds United. The gulf is already big enough and when you don't get decisions like that and your team is giving everything they've got it's a difficult one to swallow.
"There's no VAR to confirm it, it's purely subjective. I can't draw a line across it but I think [Pearson is] onside. Maybe John saw a foul in there we're not talking about.
"Little Luton, because we're playing Leeds, I feel the bitty decisions went against us. John Brooks is an outstanding referee, I'm certainly not blaming anyone here. Them things against a big team like Leeds can make the difference."
Jones felt his team's defensive shape was successful for the vast majority of the game but called Bamford's late winner a 'soft goal' to concede.
He is certain the same performance level from his men for the full duration of games will yield better results.
"We've competed with the best team in the league, if you keep giving me that we'll win games.
"You know when players are giving you everything. I've got no questions over the lads. I'd rather use it as a measurement.
"Tactically we were excellent. The game plan worked until the 90th minute. Ninety minutes is not enough."
When it came to today's visitors and the quality they possess, he had no qualms. Yet the identity of Luton's opponents and how close they came to a point made it a cruel afternoon for Jones.
"The opponent is outstanding. Some clips I didn't show the lads I think would have frightened the life out of them. They can cut teams apart when you go after them.
"Marcelo [Bielsa] is a guy I respect. I've saw his Marseille teams, his Bilbao teams, I've played against his teams, I know what they can do.
"To not get something when you really deserve something, that's what's hard to take.
"Football is cruel, there's no romance.
"Where's the football Gods when you need them? It's the least we deserve here but nobody is going to help us or feel sorry for us."