One of the 19-year-old's many surging runs led to Steven Gerrard volleying England's first goal on 51 minutes, before captain David Beckham chipped in with the second.
"If you talk to any manager in Europe today they will say that Wayne Rooney is one of the best," Eriksson told a news conference.
"He's incredible. Incredible talent and an incredible performance once again.
"I think we could have scored a lot of goals today ... we scored two and I'm very happy with that."
England beat Northern Ireland 4-0 on Saturday, with Rooney involved in two of the goals, while the Azeris lost 8-0 to Poland.
"Six points and we are still number one in the group," said the Swede. "But the important thing is to be top before the last game.
"We have two difficult away games in September in Wales and Northern Ireland and then two home games (against Austria and Poland).
"But if we go on with performances like this it won't be easy to beat us, far from it."
The England boss praised Beckham and also Azeri keeper Dmitry Kramarenko, who pulled off a series of saves to deny England victory by a bigger margin.
"If you saw the goalkeeper's performance on Saturday, you wouldn't believe it was the same person," he said. "Today he was very, very good and on Saturday everything went past him."
Eriksson regretted a yellow card for Michael Owen which will rule him out of their next qualifier against Wales and said he had taken Rooney off to ensure he would not also get a booking and a suspension.
Azerbaijan's Brazilian coach Carlos Alberto, though no fan of Owen, was impressed by England's performance.
"If they continue to improve like this, in Germany, England should be in the final," he said, adding: "They have the best midfield in the world in my opinion.
"The team has improved since the last World Cup. Tonight they were unbelievable. Their touch of the ball -- this is the kind of football I like to see."
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