Mr Nujoma’s hand-picked successor, Lands Minister Hifikepunye Pohamba, 69, is headed for victory in the presidential election.
The ruling South West Africa People’s Organisation (SWAPO) party is virtually assured a strong majority in parliament.
Voting was delayed by a few hours as some 300 polling stations, mainly around Windhoek, experienced problems with a new computerised voting system.
Long queues forming as voters waited patiently to cast their votes.
Smiling broadly, Mr Nujoma was the first to cast his ballot at a polling station off Independence Avenue in the centre of Windhoek just after voting got underway.
“I’m calling on all Namibian citizens to line up in peace and exercise their democratic rights to ensure that we continue with peace, stability and economic development,” said Mr Nujoma outside the voting station.
He said this was “irrespective of colour and status in society.”
Over the next two days, voters will choose a president and representatives to the 72-seat National Assembly in the country of 1.82 million people.
Just over 977,000 voters are to choose between seven presidential candidates and nine political parties at some 1,168 polling stations around the country.
Mr Nujoma and Mr Pohamba are founding members of SWAPO which led an armed struggle against apartheid South African rule for more than three decades.
Namibia, formerly called South West Africa, won independence in 1990 and Mr Nujoma became its first president.
The elections, the third since independence, are seen as a milestone with the departure of Mr Nujoma, who has been a pivotal figure in Namibian politics for five decades.
Mr Nujoma will retain the powerful post of SWAPO party president until 2007.
Results are expected to be announced later in the week.