Warburton's omission from interim head coach Rob Howley's side to face Italy in Rome next Saturday has been Welsh rugby's main talking point.
The Cardiff Blues flanker has struggled to recapture his best form, and the performances of stand-in skipper Jones and Justin Tipuric in the victory over France in Paris meant Howley did not even wait to discover if Warburton had recovered from a shoulder problem before making his selection.
The spotlight on Warburton's difficulty in hitting the heights of his magnificent World Cup displays was added to by Wales' wretched run of eight straight defeats.
And Ospreys forward Jones, who has led Wales on a record 30 occasions, has first-hand experience of what he is going through.
Jones was Warren Gatland's choice as Wales captain when the Kiwi took over in 2007, and he could not have had a better start in the job.
The 2008 Grand Slam was secured a matter of months later and he was quickly installed as the favourites to lead the British & Irish Lions to South Africa in 2009.
But Jones' form slumped to the extent that he did not even make the original touring party, and by the end of 2010 he had lost the Wales captaincy to Matthew Rees as the national side toiled.
The 31-year-old, one of a select group of Wales players to win three Grand Slams, has since led his country on three occasions, but has no doubt Warburton will soon be back to his best and leading from the front.
"Sam is still squad captain and he is a kid with a great future and it amazes me the reaction people have had," he said.
"It's not just Sam, some of the guys in the squad have seen their careers sky-rocket and they have not experienced the other end of the spectrum.
"Rugby careers don't go like that, the players we remember are the ones who have had that longevity and have weathered these storms, and the way to do that is not going to extremes. You can't torture yourself mentally and physically."
And Jones does not believe Warburton is feeling the weight of being the favourite to lead the Lions when they tour Australia in the summer.
"In 2009, maybe the talk of the Lions captaincy did have an effect on me, but all players know the captaincy will take care of itself. It will depend on who is going, the make-up of the team... It is not something you can control.
"It's not like a job you apply for, it's an added bonus for the person who gets it, that's what I would tell Sam."
Jones acknowledges he struggled with the weight of the captaincy, but his experiences have left him comfortable with his role as elder statesman in the current youthful squad.
When asked if he had ever felt he did not want to captain Wales during his own struggles with fitness and form, he said: "I would be lying if I said no, but you have to realise I hold it in such high esteem I would never say I did not want to do it.
"It means the world to me and it is only when you lose it you realise the value of it.
"The most difficult thing is when you are going through personal turmoil.
"It is easy to be captain when you are winning and playing well. But if you are losing, or you are winning when you are not playing well your position is called into question.
"That's difficult because you are concerned with your natural standing among the group, but it becomes easier with age. You have life experiences other than just playing, it is easier to add value in other ways."
Victory in Paris put Wales back in the Six Nations title hunt, following their opening defeat to Ireland.
England are the only unbeaten team in the tournament and Jones makes them favourites, but expects there to be a few more surprises along the way.
"It is England's to lose, they have to be favourites the way they have been going, but they have big fixtures coming up," said Jones.
"I wouldn't write France off because they will be hurting, and I would like to think we would be no pushovers in the Millennium Stadium on the final day with possible silverware on the line.
"There are plenty of twists and turns to come but we are still in the hunt.
"We face a formidable test in Italy, it will be noisy and a new environment in the Stadio Olimpico but we have to embrace it."