Geingob, 73, who ran on a platform of "peace, stability and prosperity", becomes president-elect with a massive haul of 87 percent of the vote.
"I have the honour and privilege to declare Geingob... duly elected as the winner," electoral commission chairwoman Nontemba Tjipueja announced.
In the race for the 96 seats in the legislature, SWAPO took 80 per cent of the vote in a turnout of 72 percent of registered voters.
Already an overpowering force in Namibian politics, the party managed to improve on the 2009 elections, when it received 75 percent of the vote.
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Then, the official opposition Rally for Progress and Democracy (RPD) managed to pull double figures with just over 11 percent of the vote.
But they found themselves booted from second to third place this year with only 3.15 percent of the vote, according to figures on the official Electoral Commission website.
Taking their place as the strongest opposition in parliament is the Democratic Turnhalle Alliance, with 4.8 percent.
Other African countries have run pilot or limited e-voting, but none have done so on this scale.
The African Union applauded the elections as free and fair.
Ambassador Fatuma Ndangiza, head of the AU election observer mission, on Sunday gave Namibia a thumbs up for conducting the elections in "a peaceful environment, free from violence and intimidation".
But she suggested Namibia's electoral commission "consider simplifying polling station procedures" and ensuring staff were trained in how the electronic voting machines worked.
Observers from the Southern African Development Community (SADC) also gave the vote their stamp of approval.