The new parties set to lead the government have already outlined their priorities including a review of Musharraf's US-backed policies against al-Qaeda and the Taliban.
Ahsan Iqbal, a spokesman for Nawaz Sharif, the former prime minister whose Pakistan Muslim League-N (PLM-N) party is set to become the junior partner in the new government, said "the people of Pakistan have voted for change and democracy".
"Musharraf has used the war against terror as a political tool to perpetuate his unconstitutional rule," he said before the start of the session.
The Pakistan People's Party (PPP) formed by Benazir Bhutto, the slain opposition leader and former prime minister, won the most number of seats in the February 18 parliamentary polls.
The coalition government, led by the PPP with the PML-N, plans to restore about 60 senior judges who were purged from the courts by Musharraf when he declared emergency rule last November.
Iftikhar Muhammad Chaudhry, Pakistan's chief justice, was among those forced from office by Musharraf.
The judges were removed from power to ward off legal challenges to his re-election as president by the outgoing loyalist parliament in October.
Over the weekend, Bhutto's widower and political successor, Asif Ali Zardari, signed an agreement with Sharif promising to move a parliamentary resolution on the issue within 30 days of the new government taking office.
If the judges are restored, Pakistan's Supreme Court could declare Musharraf's re-election illegal.
The coalition hopes to amend the constitution to strip Musharraf of his vast powers which includes dissolving parliament and dismissing the prime minister.
The new government also aims to axe the National Security Council which gives the military a formal say in policy-making.