The talks were to have taken place this past Tuesday but were postponed after the government sought clarification on who was on the Taliban negotiating team. Thursday's meeting, which lasted some three hours, was aimed at charting a roadmap for future peace talks to end the militants' bloody insurgency.
In a joint statement afterwards, the Taliban's chief negotiator, Maulana Sami-ul Haq, said he agreed with the government's position that both sides should avoid any steps that can disrupt the peace process.
The Taliban demands include imposition of strict Islamic law, the release of its fighters from jail and the withdrawal of government troops from northwestern tribal areas of Pakistan.
Government negotiators, who previously expressed little optimism for the talks, say they left the meeting feeling encouraged.
Thousands have died in the seven-year insurgency.