The Akhbar el-Youm newspaper did not report the full turnout but said Sisi won 21.4 million votes, and his rival Moussa Mostafa Moussa 721,000 votes, without mentioning the number of spoiled ballots.
"The voice of the Egyptian masses will undoubtedly bear witness to the fact that our nation's will imposes itself with a force that knows no weakness", Sisi said on Twitter.
"The scenes of the Egyptians outside polling stations will remain sources of honor and pride for me, and conclusive evidence of the greatness of our nation", Sisi posted on his Facebook page right after the poll closure Wednesday. The President of Electoral Commission, Shin Ibrahim, tried to mobilize voters on Wednesday with a patriotic message televised at apparent low influx to ballot box: "Show world that Egypt has always known how to make history; You are pharaohs, founders of civilization that admired world".
The election commission announced in the evening that voting was being extended by one hour, to 9.00pm (2100 GMT).
His sole challenger was Moussa Mustafa Moussa, a little-known party leader who had supported his re-election until his last-minute decision to enter the race.
In Egypt's second city of Alexandria, El-Sisi received around 88 percent of the vote, with a turnout of about 39 percent, Egypt's state news agency MENA said.
Late on Tuesday, turnout was between 15 and 20 percent, the diplomat told Reuters, requesting anonymity, with around 30 percent in some centres on Wednesday. In presidential 2014, Sisi obtained nearly 24 million votes, 97%, compared to about 760,000, 3%, which added its n competitor, Hamdin Sabahi, with a participation of 47% of voters registered.
Results of this year's vote are expected on 2 April.
At Saleh Hamad school in Shubra, only 3,500 of 12,000 eligible voters cast their votes by midday, or about 29 percent, polling judges there said.
Hussain al-Sayed, a 53-year-old tailor, did vote, although without much enthusiasm. Sisi will win anyway.
The former military commander overthrew Islamist Mohamed Mursi, Egypt's first freely-elected President, during turmoil in 2013 that followed a popular uprising two years earlier.
'I will not vote, vote for who?
The women did not say who exactly had given them money or bags of goods.
At the office of a logistics company in Cairo's working class Ward estate, employees collected national ID cards and informed people where they could vote.