Pohamba, 69, the present lands minister, is set to become Namibia's second president since independence from apartheid South Africa in 1990, replacing Nujoma, who has dominated the political scene in this southern African nation for five decades.
The final tally of results released by the election commission revealed that Pohamba had garnered 75.1% of the vote compared to 7.3% for his nearest rival, opposition leader Ben Ulenga of the Congress of Democrats.
Nujoma's ruling South West Africa People's Organisation (SWAPO) party also secured an overwhelming victory in parliamentary elections held on Monday and Tuesday, picking up a massive 75% of the vote.
Slow counting process
"We are aware that the voters were concerned about the slow counting process which lasted four days," Victor Tonchi, electoral commission chairman, said, announcing the completion of the counting process.
"The counting and verification of over 800,000 ballots each for the presidential and parliamentary elections took its time," he said.
Former President Sam Nujoma will
remain head of SWAPO until 2007
The elections held on Monday and Tuesday in the vast southern African country are a milestone as they mark the departure of Nujoma, a key figure in the country's political landscape.
The 75-year-old leader is to step down in March after 15 years in power, although he will retain the post of president of SWAPO until 2007.
During his five-year term, Pohamba will be facing one of his biggest tests of leadership with land reform, conscious that he must address fears of a Zimbabwe-style land grab.
About 4000 farmers, the majority of whom are white, own 44% of Namibia's arable land, an imbalance the government has vowed to redress with compensation and a peaceful transfer of land ownership.