He revealed that he felt 'out of control' in that Challenge Cup semi-final and that he had sought psychological help, adding: 'There's stuff that needs addressing.'
Now, that concern about his recent state of mind has led him to temporarily step down from national service.
Jones, who regards Marler as a pivotal figure in his pack, was left disappointed but impressed by what he views as a sensible decision.
An RFU statement confirmed that Marler would have been picked if available and Jones said: 'Joe played brilliantly during the RBS 6 Nations and he will be a big loss in Australia.
'Joe knows what it takes to be part of a winning international team and he obviously doesn't feel like he's quite there at the moment. We fully support Joe's difficult decision and admire his honesty.
'He's a young man with a very bright future. There's no doubt in my mind he'll use this time wisely and come back feeling refreshed and ready to be part of England again.'
Marler spoke of a 'difficult' season and added: 'After speaking to Eddie in Brighton I have decided that the best thing for me is to take a rest and not go to Australia.
'Whenever you play for England you have to be 100 per cent and unfortunately I'm not in that place at the moment. It's not a decision I've come to lightly, but I feel I would be letting my team-mates and my country down if I were to tour.
'I think a short rest will really help me recharge my batteries so I can start next season with the energy and focus that's needed to perform at the highest level.'
The England squads for the tour and the Test against Wales at Twickenham on May 29 will be revealed by Jones on Sunday.
In the absence of Marler, Mako Vunipola will step up as first-choice No 1, with Matt Mullan of Wasps as his likely under-study.
Australia coach Michael Cheika has criticised Wasps over their handling of the Kurtley Beale signing.
The versatile Wallaby playmaker will move to the Coventry-based club after recovering from knee surgery in four-to-six months, but Cheika said: 'I wasn't that keen that they dropped that press release without telling Kurtley. He would've been down that he wouldn't have had a chance to talk to (Waratahs coach) Daryl (Gibson) and he hadn't had a chance to talk to me.
'I know they've been putting a lot of pressure on him not to play Test footy either, which is happening more with the English clubs now. If he's going to be right in September and October, he'll be playing for us in the Rugby Championship, he won't be playing for Wasps. We've got clear rules in place around when you're eligible. If you're over 60 caps, you qualify. If not, you don't. So when they take these players they know that.'
'It's not a decision I've come to lightly, but I feel I would be letting my team-mates and my country down if I were to tour.
'I think a short rest will really help me recharge my batteries so I can start next season with the energy and focus that's needed to perform at the highest level.
'I wish my team-mates the very best in Australia in what is a hugely exciting and challenging series for England.'
Marler has turned to Jeremy Snape, the former England cricketer turned sports psychologist, for help in managing his temper.
Harlequins' departing boss Conor O'Shea last week told Marler to keep playing 'on the edge' despite the problems he has faced this season.
