Both senators have endorsed Carmona's opponent, Rep. Jeff Flake (R), a fact Carmona omitted from the ad.
McCain stood by his 2002 comments, when he said called Carmona "extraordinarily, perhaps uniquely qualified to address the needs of our nation."
"I am not taking back" the praise of Carmona, he said on the call.
He also said that he will not be asking Carmona to take down the ad, as he didn't expect Carmona to comply with such a request, and "I don't want to waste my time or my breath or my energy."
But he insisted that the comments he made then are irrelevant in the campaign today.
"At congressional hearings we support fellow Arizonans and we support the choice of the president," he said. "That has nothing to do with the present campaign."
McCain went on to say that Carmona would be a "rubber stamp for [Senate Majority Leader] Harry Reid," citing his support for President Obama's healthcare law, the financial stimulus and the Dodd-Frank financial reform legislation.
"I don't want my vote canceled out by Mr. Carmona's," McCain said.
He also mentioned "some allegations that were rather disturbing" during Carmona's time as Surgeon General, a reference to accusations that Carmona lost his temper and angrily banged on his supervisor's door one night, a story cited by Carmona's opponents to raise questions about his temperament.
Polls of the race have shown alternating leads for both Carmona and Flake, indicating a dead-heat just over a week out from the election.