But the attacks failed to deter Pakistanis keen to have their say.
Voter turnout was nearly 60%, the election officials said Sunday. Many people were voting for the first time.
The Election Commission secretary, Ishtiak Ahmed Khan, said the election was free and fair across much of the country, despite the problems in Karachi.
His view received qualified support from election observers from the European Union who reported that at the polling stations they visited, "polling was generally rated as satisfactory or good."
The E.U. observers said in a statement Monday that a higher rate of problems was seen in Sindh, the province where the PPP and PTI had complained of irregularities.
In Karachi, the observers said they "undertook limited observation, during which they saw some serious problems in polling and were also restricted in their activities."
They said they identified some problems in the counting of votes across the country, with 9 out of 59 stations rated as "poor or inadequate."
The national election marks the first transition between civilian governments in the nation's 66-year history. In March, the democratically elected PPP government finished serving a full five-year term.
Pakistan has experienced three military coups and been ruled by generals for about half its history.