“I will respectfully step aside ahead of the inauguration ceremony and participate in a smooth transition process,” Masisi said at a news conference Friday.
He urged his supporters to remain calm and support the new government.
The Umbrella for Democratic Change (UDC), led by human rights lawyer Duma Boko, won 25 seats, according to early counts.
The party is expected to form a government as it is expected to win 31 seats to secure a majority in parliament.
The Botswana Patriotic Front (BPF), supported by former President Ian Khama, secured five seats, and the Botswana Congress Party (BCP) has so far secured seven seats.
With Botswana’s lawmakers electing a president, Boko is likely to become the next head of state when parliament meets for the first time.
UDC supporters celebrated in the capital Gaborone and other parts of the country.
Masisi, in office since 2018, led the BDP’s failed campaign.
The president pushed the message that his party could bring about “change”, but not enough voters were convinced that the BDP could do what the country needed.
Official results are expected to be announced by the Electoral Commission later on Friday.
