"Prince Harry is a young man, we do give exits to young men when they make mistakes," Karzai, who is visiting the UK for a high-level conference, said when asked whether he thought Harry had spoken unwisely.
Karzai will also meet Prince Charles during his visit.
A long-standing friendship with Charles, whom he described as a "great representative of Britain", may have contributed to Karzai's uncharacteristic reticence.
"Prince Charles, the father of Prince Harry, is a very fine gentleman, a man for whom I have tremendous respect," Karzai was quoted by the Guardian as saying.
Pushed again about the remarks, Karzai said most people had made mistakes in their youth and shouldn't be hounded for that.
"As I said, he's a young man, and young men do make mistakes talking, while behaving, all of us have gone through that period, so let's drop it there," he said.
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Prince Harry, 28, had made the controversial comments at the end of his 20-week deployment as a co-pilot in an Apache attack helicopter stationed in Camp Bastion, in turbulent southern Helmand province in Afghanistan.
"Take a life to save a life, that's what we revolve around. If there's people trying to do bad stuff to our guys, then we'll take them out of the game," Harry had said.
"I'm not here on a free pass.....Our job out here is to make sure the guys are safe on the ground and if that means shooting someone who is shooting them, then we will do it," he said.
The Prince, who was in charge of firing the Apache's Hellfire air-to-surface missiles, rockets and 30mm gun, also had said his taste for video games helped him in battle.
"It's a joy for me because I'm one of those people who loves playing PlayStation and Xbox, so with my thumbs I like to think I'm probably quite useful," Harry said.
The Taliban, however, were quick to accuse Harry of mental illness and cowardice, joining a chorus of criticism from all sides.
"I don't believe that he participated in the fighting," Zabiullah Mujahid, a spokesman for the Taliban had said.
Karzai is visiting the UK for a trilateral meeting with the British Prime Minister David Cameron, and the Pakistani President Asif Ali Zardari, with the aim of improving fractious relations between the south Asian neighbours and ultimately pave the way for a peace deal with the Taliban.