"So whatever decision that I make with respect to General McChrystal, or any other aspect of Afghan policy, is determined entirely with how I make sure we have a strategy that justifies the enormous courage and sacrifice that those men and women are making over there, and that ultimately makes this country safer."
McChrystal earlier apologised for the controversial comments in the profile. He is quoted as criticising a senior diplomat, while his aides dismiss Barack Obama and mock his deputies.
Michael Hastings, author of the Rolling Stone article, talks to Al Jazeera about McChrystal
"I extend my sincerest apology for this profile," McChrystal said in a statement issued in advance of the article's release.
"It was a mistake reflecting poor judgement and should never have happened."
Al Jazeera's James Bays, reporting from Kabul, said McChrystal is reportedly prepared to resign over the incident.
"We understand that [McChrystal] has already offered his resignation," he said.
"He will go there for this meeting with Obama, put his four stars of a general on the table and say 'President it's up to you, I will resign if you want me to resign'.
"[But] I think most of those who see him close-up believe he is a man of honour. He will wait to see if Obama takes his resignation or decides that he is the only man to turn things around in Afghanistan."
A Nato spokesman earlier called the article "rather unfortunate", but said McChrystal has the full support of Anders Fogh Rasmussen, the Nato secretary-general.
Speaking from the Belgian capital, Brussels, James Appathurai told Al Jazeera: "Nato still has full confidence in General McChrystal."
"I think it's important to remember that these are commanders in the middle of a war zone, under enormous stress."
The Afghan government also expressed hopes that McChrystal would keep his job despite the furore.
General Mohammad Zahir Azimi, a defence ministry spokesman, said there had been great improvements since McChrystal took command of Nato's International Security Assistance Force (Isaf) last year.
"For instance, civilian deaths have decreased and we are still working together with General McChrystal to further reduce this," Azimi said.
On Tuesday, a spokesman for the Afghan president said Hamid Karzai considered McChrystal the "best commander" of international forces during the nearly nine-year war in the country.
In the magazine profile, McChrystal jokes sarcastically about preparing to answer a question referring to Joe Biden, the US vice-president, known to be a sceptic of the commander's war strategy.
He also told Rolling Stone that he felt "betrayed" by Karl Eikenberry, the US ambassador to Kabul, in a White House debate over war strategy last year.
Referring to a leaked internal memo from Eikenberry that questioned McChrystal's request for more troops, the commander said that the ambassador had tried to protect himself for "for the history books".
"I like Karl, I've known him for years, but they'd never said anything like that to us before," McChrystal said in the article.
Eikenberry, himself a former commander in Afghanistan, had written to the White House saying Hamid Karzai, the Afghan president, was an unreliable partner and that a surge of troops could draw the US into an open-ended quagmire.
Al Jazeera's James Bays reports on the article that sparked the controversy
The article revisits the friction between the White House and the military last year as Obama debated whether to grant McChrystal's request for tens of thousands of reinforcements.
Al Jazeera's James Bays, reporting from Kabul, said that McChrystal managed to offend every single one of his important bosses with the statements in the article.
He said that the Rolling Stone reporter managed to get high-level access.
"I met the reporter in Washington DC over a month ago after he came out of a meeting inside the White House with McChrystal's advisers," our correspondent said.
"This incident shows the tensions that exist between the top advisers here in Afghanistan. What will happen now is how this agreement is viewed on Capitol Hill and on the Afghan street.
"The Taliban is also trying to win over the Afghan people. There is certainly very little disunity normally in the Taliban."