The final official count is expected late on Tuesday.
Although Musharraf was not on the ballot, Monday's election was widely seen as a referendum on his eight-year rule, including his alliance with the US in its "war on terror", which many Pakistanis oppose.
If the opposition seizes control of parliament, Musharraf, who first took power as an army general in a 1999 coup, could be forced to step down.
Two of the president's close allies, Chaudhry Shujaat Hussain, the PML-Q chairman, and Sheikh Rashid Ahmed, the outgoing railway minister, lost their seats in Punjab, the most populous province and a key electoral battleground.
Musharraf said he would work with the new government regardless of which party wins.
- Pakistan has 81 million registered voters, out of a population of 160 million people.
- Voters choose 272 members of the National Assembly, or lower house of parliament, for a five-year term.
- Another 60 seats are reserved for women and 10 for religious minorities.
- There are 106 parties, 15 of which were represented in last parliament.
- More than 60,000 polling stations were set up across the country.
- Key issues include restoration of full civilian government, reinstatement of sacked judges, rising militancy, economy and high unemployment.
"I will give them full co-operation as president, whatever is my role," he said after voting in Rawalpindi.
"Confrontationist policies ... should end and we should come into conciliatory politics in the interest of Pakistan. The situation demands this."
A spokesman for the PML-Q, which dominated the outgoing parliament, conceded that early results showed a "big gain" for the opposition.
"If the results are confirmed we will play the part of the opposition as effectively as we can," Tariq Azeem said.
"We congratulate Nawaz Sharif [the PML-N leader] for an excellent performance by his party and we also congratulate Asif Ali Zardari [the PPP leader]."
Despite international attention and the polls seen as a referendum on Musharraf's rule, apathy and fear kept millions of voters at home on Monday.
The national turnout was estimated at 40 per cent of Pakistan's 81 million eligible voters, a senior elections official said on Tuesday.
Sarwar Bari, of the non-profit Free and Fair Elections Network, said his group's 20,000 election observers reported a voter turnout of about 35 per cent, the same as in the 1997 election and the lowest in Pakistan's history.
Ayaz Baig, the election commissioner in Punjab, estimated the turnout there to be at between 30 per cent and 40 per cent, slightly lower than in the 2002 election.
In Baluchistan and Sindh provinces, turnout was estimated at about 35 per cent, officials said.
Nearly 80,000 troops backed up police across the country to provide protection against expected attacks by pro-Taliban fighters, but aside from a few instances of violence, there was relative clam, Al Jazeera's Kamal Hyder said from Lahore.
Still, at least 24 people were killed in election-related violence, mostly in Punjab.
The PPP said 15 of its members had been killed and hundreds more injured in scattered violence "deliberately engineered to deter voters".