Altitude at Ellis Park.....are the effects really so severe.

I was struck by the fact that Argentina played Ecuador in Quito at 9300 feet in the WC soccer qualifying.....and these presumably mostly sea level warriors never faded. So what’s the deal here, soccer is the harder sport for endurance. .. Well Quito at 9300 feet has 14.5% oxygen. Whereas Johannesburg at 5700 feet has 17% oxygen.....not a proportional drop in Quito but still significant. At sea level the effective oxygen is 21%. So Quito has another 60% or so drop relative to J’burg. .. CURIOUS.

 Moz, my guess would be muscle mass. Probably something to do with recovery times. Bigger guys have longer recovery periods. IE when the tank's empty, it's empty. 
Smaller guys with quicker recovery times would be able to control anaerobic rhythms more efficiently and so there would be less noticeable difference. Rugby players, especially the forwards are forced into moments of high exertion. If you match your opponent on five occasions but fail due to fitness on the sixth occasion...there's big advantage there.
It's probably a case of having to do 1km run. Guy A jogs the full distance while guy B sprints 100m then walks 100m until the end. My guess is that guy B would not be able to go on for nearly as long as guy A.
So if a rugby team trains at altitude, a proven advantage across various sports then it makes sense that the difference between between that team and the sea level team would play a substantial role in the final quarter of matches. Over a longer period the same difference would probably also be noticeable between to soccer teams.
Pure speculation of course.

I think that’s accurate Plum, it’s a different kind of exertion and we see the effects of altitude in Kenyan and Ethiopian long distance runners. I was just speculating that by now there is a mental component as well....you know you are supposed to be tired....so you are tired.

 Indeed Moz. And the whole thing is probably exasperated by the altitude team causing the sea level team to gas via whatever means and then forcing them into mistakes. Another guess, but it's probably true that a frantic and panicking individual uses more energy to carry out the same task as someone who is calm. 
Could be why so many teams did well against the Lions until the last 30 minutes and then seemed to fall apart. 

When you're knackered and suddenly your opposition are spreading the ball from side to side as though it's the 10 minute of the game...that can't be good for the body or the mind. What's one's state of mind like after they then go and score a couple of quick ones. Psychological unravelling haha.

 Moz,I see this somewhat differently.Nitrogen and oxygen do not differ much (mol mass 28 vs 32) and thus is a homogeneous mixture in air. Quito, Johannesburg or any other place has the same composition ca 20% oxygen and 80% nitrogen (ignore the noble gases and other trace gases) . An athlete at Johburg or in say Durban will inhale air with the same composition. The difference however lies in the decreasing density of air with altitude. A breath of air of say 250 millilitre will contain more oxygen (and nitrogen) at sea level than at altitude. I understand that the body will compensate for this lack of oxygen by producing more hemoglobin to get enough oxygen to the body - this is why mountain climbers must stay at certain heights to give their body time to acclimatize. Same in rugby.

Thanks for that correction Blikkies, I was reporting ‘effective oxygen’ from a table on a climbers site....and as you point out it’s the body’s varying ability to use oxygen that’s being translated into effective oxygen levels at various altitudes.

Interesting discussion Mozter. I am very much into UFC and mixed martial arts, and it is common knowledge in the sport that carrying muscle comes at the expense of endurance. Just to add credence to what Plum has said. IF you watch MMA you'll notice that 90% of the most successful fighters are very lean and not overly muscular. In fact, these guys often make a concerted effort to reduce muscle mass. An example is Nate Diaz, who famously beat Connor McGregor in their first fight. He looked slightly chubby, and Connor even commented on that fact in the fight build up. However, Diaz is also a triathlete that is known for his excellent stamina. It was that stamina that eventually lead to Conor's undoing. In other words, even fat appears to have less effect on stamina than muscle mass.  

This isn’t just an excuse for your lack of muscle mass Bloo? Slightly chubby....hmmm. .. Only kidding. I guess what you say means forwards would tend to feel the effects more than backs.

Shart...you're onto me! LOL
Nah, I am only 38 and still in pretty decent shape. I'm also relatively tall 190cm's, so when I do slack off a bit on the diet/exercise front, people mostly don't even realise I have gained a few pounds.   

Enjoy those years Bloo...a few pounds can always be shed, it’s regular exercise that counts.

 More about attitude than altitude I recon.