Commission chairman Mamduh Marai told reporters in Cairo on Friday that incumbent Mubarak's win was based on a turnout of 23% of registered voters.
Mubarak received 6,316,714 votes (88.6%).
Second place went to Ayman Nour of the opposition Al-Ghad party, with 540,405 votes (7.3%).
The other main opposition candidate, Noaman Gomaa of the Wafd Party, received 201,891 votes (2.8%).
Before Wednesday's election, officials in Mubarak's ruling party had said they hoped at least 30% of the 32 million registered voters would cast ballots.
Mubarak, 77, has been in power since 1981, when he succeeded the assassinated Anwar Sadat.
Since then, he has been elected through referendums in which Egyptians could only say yes or no to a single parliament-nominated candidate.
The election was the first ever in which Mubarak faced a competitor after years of being re-elected in "yes-no" referendums in which he was the sole candidate.
Nour won 7.3% of the vote
His government has touted the change as a major democratic reform, and as a candidate Mubarak promised further change.
But opponents were sceptical, with most major parties boycotting the election.
Widespread violations were reported by voters, opposition groups and independent monitors during the balloting - particularly strong pressure from officials and other on voters to back Mubarak.
But the election saw none of the violence or overt vote rigging that has plagued past parliamentary elections.
Marai, who is the top judge on Egypt's highest court, said the vote was clean and that allegations of violations came out of "over-enthusiasm in a nascent experiment that will be the cornerstone in the construction of democracy".
On Thursday, Nour demanded the election be repeated because of the allegations, but the commission - which reform-minded judges have accused of being dominated by the government - rejected the request.
Third-place finisher Gomaa on Friday said his party would put together a list of the election violations it witnessed and present them to the commission. But, speaking to Aljazeera, he acknowledged that the violations were not enough to affect Mubarak's victory.