Jones was very tired by the end of the 1st against Shogun, it then took him until halfway through the 3rd to finish the fight. He got knackered in less then 3 rounds, taking hardly any damage, trying to finish a fighter even more tired than he was.
Defeating Rua via TKO in the 3rd is impressive on paper, however watching the fight, the fact he didn't finish it in the 1st is very unimpressive. Doesn't matter if it is Shogun, he had a fighter hurt and losing energy fast early in the first round, and then he himself gassed without even taking damage and took another 2 rounds to get it done.
I think that you are too harsh on Jones here. It does matter that it was Rua/ an elite fighter at a way higher level than his past opponents. Yes, Rua was hurt early, but not in a way to get shut down easily. With his experience Rua was always dangerous to Jones which the latter could only neutralise by putting constant pressure on his opponent (and by quite intelligently disrupting his opponent's rhythm). Because of the pressure, from both sides, it was a very exhausting fight for both fighters. Had Jones gone more for an early finish he really would have risked to gas and be overcome if Rua had managed to bounce back into the game.
The way Jones fought that fight was the optimum he could do with his current skills and abilities (which probably will still improve). I think he couldn't have done it otherwise without raising the risks very much. If he had lowered his pace focussing on a 5 round fight he would have left openings for Rua to imply his game and if he had looked for the finish earlier he would have risk to really gas.
So for the original question whether Jones would survive five rounds. In a fight similar to the Rua fight, without getting a TKO in Round 3, I think Jones would get into trouble in the later rounds. The constant pressure would take its toll, but Machida is not Rua. Machida's fighting style is different from Rua's. Jones wouldn't need to put the same constant pressure on Machida as he did on Rua. So if he is intelligent/cautious enough to pace himself, Jones has a very good chance of surviving five rounds with Machida.
However I also think that Machida with his fighting style could have one of the best chances to win against Jones if he can avoid major damage due to his elusiveness and bring good counters. In a pure pressure vs. pressure fight it seems that no one can compete with Jones at the moment (besides a lucky punch).