Moody's leadership was criticised by England's elite rugby director Rob Andrew and some of his team-mates in confidential World Cup reports that were leaked to The Times.
The veteran Bath flanker was criticised by an unnamed team-mate for having too much contact with his agent, Mark Spoors, during the tournament.
Moody, who cancelled a book signing at Twickenham today, was also singled out by Andrew for leading a senior player delegation that disputed the squad's World Cup payments.
Moody released a statement on Wednesday rejecting the reported claims that he was motivated by money.
Johnson told Press Association Sport: "Lewis was the outstanding choice to captain of that group and I wouldn't hesitate to make the same choice again to do that.
"He was fantastic. He worked incredibly hard on and off the field, he did the job as well as he could do it. He gave a huge amount of care and thought to what he was doing. He didn't try and be something that he isn't.
"If some people didn't think he was a good captain, fine, but that is certainly not the majority view of the team. If you take one opinion and one comment and chuck it out there...
"You can't fault Lewis for the way he captained that squad.
"He was coming back from injury and that was difficult for him in that sense and he was hugely frustrated at times about where he was physically and not being able to be on the field, leading the team.
"I thought he did an absolutely fantastic job from the day we asked him to step up and do it."
The published excerpts from the leaked World Cup reviews paint the picture of a dysfunctional England squad, riven by a lack of trust and motivated by money ahead of ambition.
Johnson, who resigned as team manager last week, spoke out yesterday in defence of his regime, insisting the reporting had been selective and did not accurately represent the culture of the squad.
Johnson has no problems with players being motivated by money but he does not believe his squad prioritised commercial opportunities ahead of their rugby.
"That is a personality thing. It is not new. If your motivation is money and that makes you play well, I have got no issues with that," Johnson said.
"I have played with a lot of players and part of the motivation was getting paid well and they had been amateurs as well. It is fundamentally what you bring and how you bring it.
"Commercial pressures at top-end sport are there. You have sponsors, they are important to the game and you do that right. But you need to get the balance right in your life as a player.
"You can go around chasing those things and it can get in the way if you get the balance wrong.
"That is something we are trying to be aware of all the time. We have our commercial partners as well. For any team it is a balance."
Johnson did not believe England got the balance wrong.
"I think players are pretty much similar to what players have always been. The influences around them in society are certainly different," he added.
The reports were compiled by the Rugby Football Union, the Rugby Players' Association and the Aviva Premiership clubs with recommendations set to be proposed to the RFU board on November 30.
The Times has published anonymous player quotes which imply a split in the camp and reveal a level of frustration with Johnson's coaching team.
Brian Smith, who stood down as attack coach on Thursday, and defence coach Mike Ford also came in for criticism.
Johnson was accused of poor selection and for not ruling with the authority many felt he should have.
"Players gripe about coaches," Johnson said.
"We all did it as players. If there are any givens in life, that is one of them. This is not a popularity contest and it is not a democracy most of the time.
"Reports of the management group not liking each other are completely false. That couldn't be further from the truth."
Even if the reporting is not balanced, as Johnson argued, the published comments suggest there was at least an undercurrent of dissatisfaction with the way their controversy-dogged campaign was run.
England crashed out in the quarter-finals and Johnson said: "I hope there is dissatisfaction because we didn't do what we wanted to do in the tournament.
"There were things we highlighted as potential pitfalls that we fell into on and off the field. There is dissatisfaction that we could have gone further in the tournament and win.
"I have got no problem taking criticism on the chin. In fact I welcome it far more than praise - but you just get to the point of going 'that can't go unchecked because it is so inaccurate that it is just wrong'.
"It is not a personal thing (that I have spoken up). It is for the game and for the team.
"You want the team to be held up as a great example for rugby players and sportsmen and that is clearly not the case at the moment and you have got to put that right."