North Korean authorities arrested Ling, 32, and Lee, 36, in March, saying they had crossed the border with China illegally "for the purpose of making animation files to be used for an anti-DPRK [North Korea] smear campaign over its human rights issue".
The two who worked for the California-based Current TV co-founded by Al Gore, who was Clinton's vice-president, were found guilty after a trial and sentenced to 12 years of hard labour in June.
The reporters' families said they were "overjoyed" by the pardon and "so grateful to our government … for their dedication to and hard work on behalf of American citizens".
"We especially want to thank President Bill Clinton for taking on such an arduous mission and Vice-President Al Gore for his tireless efforts to bring Laura and Euna home.
The visit by Clinton, who is also the husband of Hillary Clinton, the US secretary of state, is the highest-profile US contact with North Korea since he was president nearly a decade ago when his secretary of state, Madeleine Albright, went there in 2000.
|State media said Kim and Clinton held an 'exhaustive conversation' [AFP]
Clinton was greeted warmly on his arrival and had what KCNA described as an "exhaustive conversation" over dinner with Kim and his senior aides.
State media said Clinton apologised on behalf of the women and relayed a message of gratitude from Barack Obama, the US president.
"Clinton expressed words of sincere apology to Kim Jong-il for the hostile acts committed by the two American journalists against the DPRK after illegally intruding into it.
"Clinton courteously conveyed to Kim Jong-il an earnest request of the US government to leniently pardon them and send them back home from a humanitarian point of view," KCNA said.
The state news agency added that the visit would "contribute to deepening the understanding between the DPRK and the US and building the bilateral confidence".
But the White House had a different view, saying that reports of a message from Obama were "not true" and taking pains to emphasise the private and limited nature of Clinton's trip.
David Axelrod, an adviser to Obama, told MSNBC that Clinton was on a "private humanitarian mission" and that "I don't think it's related to other issues".
Clinton's visit had raised speculation that he may discuss other issues with the North Koreans such as getting back to negotiations over their nuclear programme.
"Clinton expressed words of sincere apology to Kim Jong-il for the hostile acts committed by the two American journalists"
Christopher Nelson, an Asia analyst in the US who edits the Nelson Report on international affairs, told Al Jazeera that more needed to come from Clinton's visit than the release of the journalists for it to be considered a success.
He said the North Koreans "definitely wanted the propaganda coup of getting [Clinton] to go there and show respect to Dear Leader - to the leader of North Korea - and … they got that in spades".
"So people here [in the US] are worried, with cause, that if all we get are the two women being returned - and we're personally thankful for that, of course - then maybe we gave the North Koreans a little too much."
"We'll need to see 'what next'. Did sending somebody of the stature and importance of Bill Clinton, does that serve as a door opener, a bridge opener ... a face-saving vehicle for the North Koreans to come back to talks about denuclearisation?"
The journalists' release followed weeks of quiet negotiations between the US state department and the North Korean mission to the United Nations, said Daniel Sneider, associate director of research at Stanford University's Shorenstein Asia-Pacific Research Centre.
|The women looked to be in good health as they left North Korea on Wednesday
Clinton "didn't go to negotiate this, he went to reap the fruits of the negotiation", Sneider told the Associated Press.
Pardoning Ling and Lee and having Clinton serving as their emissary served both North Korea's need to continue maintaining that the two women had committed a crime and the Obama administration's desire not to expend diplomatic capital winning their freedom, Sneider added.
Relations between North Korea and the US have worsened following Pyongyang's second nuclear test on May 25 and consequent United Nations sanctions.
North Korea pulled out of six-party talks on its nuclear programme, expelled nuclear inspectors and test-fired a barrage of missiles in defiance of the sanctions.
It also repeatedly issued bellicose rhetoric against South Korea and the US, but indicated last week that it was open to direct talks with Washington.
The US, however, has maintained that the six-party arrangement is the appropriate forum for dialogue.