"Our political leadership, our ministers and our army chiefs met and evaluated today our security situation. I don't think this nature of meetings have taken place anywhere at any time."
Kabul has repeatedly accused Islamabad of not doing enough to stop fighters crossing the border to carry out attacks, but ties have improved under Zardari as he battles growing violence in the tribal regions along the border with Afghanistan.
A joint declaration following the meeting said representatives from Afghanistan and Pakistan, along with officials from Turkey, would continue contacts "in functional and comprehensive formats on various levels".
Military and intelligence officials will meet once a year as part of delegations led by foreign ministers, it said.
Karzai and Zardari also asked Abdullah Gul, Turkey's president, to organise a summit aimed at boosting regional co-operation.
The meeting came after the US unveiled a new strategy for the region which treats Afghanistan and Pakistan both as part of the came challenge.
Barack Obama, the US president, has pledged to send 17,000 additional troops to Afghanistan and 4,000 advisers to train its security forces.
His plan will also channel additional funds to Kabul and Islamabad.