More than 600 Pakistani and Afghan tribal elders had gathered for the peace talks which looked at the increased fighting on the two countries' border.
Al Jazeera's correspondent in Islamabad, Kamal Hyder, said: "A lot of people here are asking if this is too little, too late.
"Musharraf and Karzai have both become unpopular in their own countries and many people say this jirga is not going to achieve anything."
The jirga began deliberations on Thursday. Delegates had split into committees focused on topics such as the reasons for "terrorism", the fight against drugs - said to finance militants - and good neighbourliness, spokesman Asif Nang said.
The results of these findings are expected to help the formation of a strategy, to be announced on Sunday, before Musharraf and Karzai were to close the meeting, the spokesman said.
Recommendations are likely to include the establishment of a joint commission to analyse factors fuelling terrorism and another on fighting the drugs trade and organised crime, Afghan media reported on Sunday.
Two of Pakistan's seven tribal areas refused to send delegates, citing the lack of Taliban representation and saying there could be no solution without the group.
Karzai said the jirga would cement relations between Afghanistan and Pakistan.
A Pakistan news agency quoted him saying: "Assembling leaders and public opinion-makers from both the countries to discuss and share their views on core issues is a good omen for peace and harmony in the region,"
The two countries have long accused the other of not doing enough against anti-government fighters.
Relations between Karzai and Musharraf have been particularly strained over the resurgence of the Taliban, which was driven from government by US-led forces in 2001 after having been helped to power by Pakistan in 1996.