England's fifth successive 3-0 win in Group E meant that if they beat Russia in Moscow on Wednesday they will qualify for the trip to Austria and Switzerland.
Rooney said before the Estonia game that he had not played at his best for England for some considerable time, while McClaren said the 21-year-old striker was "potentially world-class" but still had a long way to go to get there.
The comment clearly inspired Rooney, making his first England appearance for seven months, to have an excellent match.
He foraged deep in midfield, ran at defenders, linked well with Michael Owen in attack and crowned a very good afternoon's work when he turned and fired home a left-foot shot from a Joe Cole cross to put England 2-0 up after 32 minutes.
It was his first goal in 16 competitive matches for England since he scored two against Croatia in Euro 2004 in Portugal.
McClaren said afterwards: "When players of his standard receive criticism, they have to prove themselves on the pitch. That is exactly what Wayne did, and now he has to do it consistently.
"He admitted himself that he had a point to prove and he has gone a long way to doing that.
"We all know Wayne is a threat and I repeat, he has the potential to be world class. I am delighted with his goal but his overall contribution to the team was very good. He got better and better as the game went on."
England were 3-0 up after 33 minutes and although they did not maintain their high tempo start to the match, the points were secured.
Croatia top the table with 26 points from 10 matches, England have 23 from 10 and Russia 18 with a match in hand.
Russia can still pip England but even if Russia win on Wednesday, England will still qualify as long as they beat Croatia in their final match at Wembley on November21, no matter what Russia do in their final matches away to Israel on November17 and Andorra on November21.
If Wednesday's match is drawn, England would need a draw against Croatia to qualify.
Chelsea defender Ashley Cole was withdrawn from the squad on Sunday after picking up an ankle injury in the win over Estonia with Middlesbrough's Luke Young brought in as a replacement.
There is also a fitness worry over defender John Terry, who missed the Wembley triumph because of a knee injury.
