Wallabies skipper Mortlock had a chance to win it right at the death, but his 50-metre penalty sailed wide and England progressed to a last-four meeting with France.
"There's certainly a lot to be proud of: resolve, stubbornness, not giving in to anything," Wilkinson said.
"Saturday was a real joy to be part of. One of the best days of my life."
However, the Newcastle fly-half spared a thought for Mortlock, who was clearly distraught at full-time in Marseille.
"For all that, there was one moment over which we had no control: Stirling Mortlock's penalty attempt in the 78th minute.
"I saw that kick again on a replay that night and I can tell you: it was a damned fine kick. With the balls flying the way they are he has real sympathy from me there, that is for certain.
"As a kicker here you are not completely accountable. Sometimes it is like you are almost hitting and hoping, and kickers just never do that."
Wilkinson's sympathy may be borne from issues he has with his own kicking.
"This is a difficult subject and I don't want to make a big deal out of it. But in kicking you naturally want to control as much as you can; you can't ever control the wind and you can't control the pitch conditions. It seems that, at this tournament, the ball is another one of those.
"When you can't control something like that, it's very difficult. And I know it is the same for everyone and I am also aware that some kickers, Chris Paterson notably, have been extremely successful.
"But for me, I feel I've got a few kicks right in this tournament and still been punished by seeing them go wide. On Saturday I missed three from seven; one of those I knew immediately I'd executed wrong, but I was happy with the other two.
"Don't get me wrong, I am not mentioning this as a hard-luck story.
"The wind on Saturday was very tough, the flags on the top of the stadium told a different story to those at pitchside and the wind changed a couple of times when we were down there too. That makes kicking here really tough mentally. If the ball moves in mid-flight, you have to work out if it is the wind, the ball or yourself.
"Don't worry. I'll be back down to the training ground trying to figure all that out. The good news is I've now got another week to perfect it."