The polls closed at 5 p.m. local time, and results in the vote for a new National Assembly and provincial assemblies were expected to emerge Tuesday.
The vote was delayed six weeks after former prime minister and main opposition leader Benazir Bhutto was assassinated in a political rally on Dec. 27.
Bhutto's Pakistan Peoples Party and former Prime Minister Nawaz Sharif's Pakistan Muslim League were expected to do well in the elections, and an overwhelming win over the pro-Musharraf party -- the Pakistani Muslim League-Q -- could leave Musharraf politically vulnerable and even at risk of impeachment.
Musharraf, an ally in the U.S. war on terrorism, was re-elected in October to a five-year term, but his popularity has eroded by what some Pakistanis considered strong-arm tactics, such as imposing emergency rule in November and reconfiguring the Supreme Court.
Pakistanis also blame the government for rising prices, food shortages and frequent power outages.
Musharraf urged reconciliation after casting his vote in Rawalpindi, where Bhutto was killed.
"Whichever political party wins, whoever becomes prime minister ... I congratulate them and I will fully cooperate with them as president," he told reporters, according to Reuters.
Opposition party leaders vowed mass protests if there appeared to be any vote-rigging.
Meanwhile, violence on the day of elections was lower than expected. At least eight bombs exploded Monday in Pakistan's northwest and southwestern regions but caused no casualties, officials told Agence France-Presse.
On Saturday, a suicide car bomber rammed into a crowd of Pakistan Peoples Party supporters in the northwest tribal town of Parachinar, killing 47 people and injuring more than 100, according to the AFP.
Despite fears of more violence, which might have kept some Pakistanis from going to the polls, election official Mohammad Farooq estimated turnout at 35 percent at his polling station in Rawalpindi.
"Considering the security circumstances, that's good," he said as the polls closed, Reuters reported.
In five elections since 1988, voter turnout has typically been between 30 percent and 40 percent, according to Bloomberg News.