The 40-year-old lawyer was beaten by ruling National Democratic Party candidate Yehya Wahdan in his own Cairo stronghold of Bab al-Shariya, commission secretary-general Intissar Nessim announced on television on Thursday.
Nessim was announcing partial results from the first round of elections that kicked off on Wednesday in 82 constituencies across Egypt.
Nour rose to prominence and attracted international attention after being remanded in custody for six weeks earlier this year over forgery charges he said were trumped up to undermine his political ascension.
In September, Nour had emerged as the strongest of the eight candidates who challenged Mubarak, by mustering 7.6% of the vote against the veteran president's 88.6%.
Since then, his party has been plagued by internal dissent he charged was engineered by the government to weaken his parliamentary campaign, which was also hampered by his forgery trial.
Nour, who also lost his father during the campaign, was under no illusion that he would retain his seat.
"I'm sure he will not be re-elected. The regime will resort to its old methods. It's very important for them not to let him have more political legitimacy," his wife and spokeswoman Gamila Ismail had told AFP before the campaign kicked off.
Beyond ousting Nour, Mubarak's National Democratic Party took a strong early lead in the first results from the legislative elections.
Muslim Brotherhood fielded more
than 100 candidates nationwide
Leading NDP figures, including parliament speaker Fathi Sorour and Minister of State People's Assembly Affairs Kamal el-Shazli, held their seats, the election commission said.
The NDP won 13 of the first 14 seats declared on Thursday morning.
The Muslim Brotherhood, which was the largest opposition group in the outgoing parliament and is fielding more than 100 candidates across the country, said it had won three seats in other constituencies but these were not confirmed.
In many of the 164 seats at stake in the first stage, the top two candidates will go into a second round next Tuesday because neither of them won 50% of the vote.
Some constituencies had more than 20 candidates, in many cases including former NDP members who failed to obtain the party's nomination and broke with party discipline to challenge the official NDP candidate.
After winning in previous elections, such independents have usually rejoined the ruling party.
The voting on Wednesday was in Cairo, the central provinces and two remote areas.
Mubarak's governing NDP party
has taken a strong early lead
Other parts of the country will vote on 20 November and 1 December, with second-round run-offs six days later.
The final result may not come out until the middle of December.
Monitoring groups and opposition parties reported widespread irregularities, including intimidation, vote-buying and the use of government vehicles to take people to vote en masse.
The Independent Commission for Election Monitoring said the average turnout was 34% but election officers in a hotly contested Cairo constituency said on Wednesday it ranged between 10% and 20% in the various polling stations.
Meanwhile, the Arab Committee for the Defence of Journalists has condemned an assault on Aljazeera correspondent Ahmad Mansour in Cairo.
Mansour was attacked by two unidentified persons in front of Aljazeera's office in Cairo on Wednesday.
The committee expressed solidarity with Mansour and called on the Egyptian authorities to investigate the incident.
"Assault incidents on journalists in Egypt have continued for years without the perpetrators being brought before courts," the committee added.