After a crisis meeting with McChrystal over the contents of the article, Barack Obama, the US president, announced on Wednesday that the general's conduct had been unacceptable and removed him from his post.
'No change in policy'
But Obama said McChrystal's departure would not signal a change in approach towards the Afghan war.
"This is a change in personnel, not a change in policy," he said.
"We will not a miss a beat because of the change in command in the Afghan theater."
Vowing that he would not tolerate any further discord among those commanding the war , Obama said he would insist on "a unity of purpose on the part of all branches of the US government".
"I'm paying very close attention," he said. "And I will be insisting on extraordinary performance moving forward."
Speculation that the change of command would signal a change in policy was played down on Thursday as military officials reaffirmed their commitment to the current strategy.
Robert Gates, the US defence secretary, cautioned that McChrystal's removal should not be misinterpreted.
"No one, be they adversaries or friends or especially our troops, should misinterpret these personnel changes as a slackening of this government's commitment to the mission in Afghanistan," he said on Thursday.
"We remain committed to that mission and to the comprehensive civil-military strategy ordered by the president to achieve our goals there."
"The strategy hasn't changed and the policy hasn't changed and we are very focused on the time between now and July 2011"
Admiral Mike Mullen,
Chairman of US joint chiefs of staff
McChrystal has overseen the arrival of 30,000 new troops this year, many of whom are engaged in trying to secure Afghanistan's volatile southern promises. Plans are in place to begin withdrawing troops next summer.
Admiral Mike Mullen, the US military's most senior officer, said he supported the decision to remove McChrystal from his post, but insisted that the war effort was on track.
"The strategy hasn't changed and the policy hasn't changed and we are very focused on the time between now and July 2011," he said.
Anders Fogh Rasmussen, the Nato secretary-general, released a statement saying the approach was correct, despite foreign troops having just endured their bloodiest month since the war began in 2001.
"I have taken note that General McChrystal is stepping down as commander of the Nato-led mission in Afghanistan," Rasmussen said.
"While he will no longer be the commander, the approach he helped put in place is the right one.
"The strategy continues to have Nato's support and our forces will continue to carry it out."
In Kabul, General Mohammad Zahir Azimi, a spokesman for the Afghan defence ministry, also voiced his support for the strategy put in place by McChrystal.
"Since General McChrystal took over the job as commander of the international forces, there have been a lot of changes in different departments, which are very important and positive,'' he said.
"For example, there has been a decrease in the numbers of civilian casualties and we're still working jointly with McChrystal to decrease it further."
Al Jazeera's Patty Culhane reports on General David Petraeus, McChrystal's successor
Al Jazeera's James Bays, in the Afghan capital Kabul, said that behind the scenes, the Obama administration knows that Petraeus faces a difficult task in taking over the command at a crucial point in an intensifying conflict.
"He has been looking at this war from afar, but right now at the height of the battle he has got to take over on the ground," our correspondent said.
"It will be difficult. He's got to get to know the key figures here."
Prince Ali Seraj, president of the National Council for Dialogue with tribes of Afghanistan, said policy is more important that personality in Afghanistan.
"The personal change in Afghanistan is not going to have any effect on the policy change in Afghanistan," he told Al Jazeera.
"The general feeling in Afghanistan is that regardless of who comes to lead the international forces in Afghanistan, it is the policy that is going to have the effect."
McChrystal's shock departure follows the release of the Rolling Stone article on the internet on Tuesday, which contained quotes critical of Joe Biden, the US vice-president, and several other high-ranking officials.
At one point, McChrystal referred to a leaked memo from Karl Eikenberry, the US ambassador in Kabul, which questioned the competence of the Afghan government.
Michael Hastings, author of the Rolling Stone article, talks to Al Jazeera about McChrystal
"Here's one that covers his flank for the history books," McChrystal said. "Now if we fail, they can say, 'I told you so.'"
After being removed from his post, McCrystal emailed a short statement to reporters saying it had been a "privilege and an honour" to have served as commander of the international forces in Afghanistan.
"I strongly support the president's strategy in Afghanistan, and am deeply committed to our coalition forces, our partner nations and the Afghan people," he wrote.
"It was out of respect for this commitment that I tendered my resignation."
Until Petraeus is confirmed by the US senate, Lieutenant-General Nick Parker, the British deputy commander of the Nato-led forces, is assuming command of the troops, according to David Cameron, the UK prime minister.
It is unclear how long the transition will take.