The Pakistani leader had originally been due to attend the opening of the conference on Thursday, but withdrew, citing important engagements in Islamabad.
Dan Nolan, Al Jazeera's correspondent in Afghanistan, said the Musharraf's change of heart came after pressure from the the United States.
"The idea for the jirga came about at the White House between Bush, Karzai and Musharraf, and as a result, the US is interested in the outcome of the jirga," he said.
About 700 Afghan and Pakistani tribal elders, religious clerics, parliamentarians and other figures - many from the troubled border area, are present at the jirga.
The four-day meeting aims to come up with a common approach to preventing al-Qaeda and Taliban activity, although analysts say it is unlikely to have much impact.
Fresh fighting across Afghanistan however has marred the 'peace jirga', leaving at least 45 people dead including a British soldier.
Taliban fighters ambushed a joint Afghan and Nato army convoy, sparking a battle that killed seven Afghan soldiers and 20 fighters, the defence ministry said.
General Mohammad Zahir Azimi, an Afghan army spokesman, said: "The militants ambushed our convoy," adding that the army called in Nato warplanes to bomb the fighters' positions after the attack.
"We called in friendly forces' air power. Seven Afghan soldiers were martyred in the ambush and 20 enemy elements were also killed."
The latest death brings to 129 the number of international troops killed this year, according to an AFP count. More than 190 were killed last year.
About 50,000 international troops, more than half of them Americans, are deployed in Afghanistan.