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Over the last year, Uber has also pulled out of Ivory Coast and Tanzania. The latest announcement means Egypt, Ghana, Kenya and South Africa are the only African countries in which the firm now operates.
"This decision is limited strictly to these two markets and does not impact our operations across the rest of the continent," Uber's statement to the BBC said.
"We remain committed to sub-Saharan Africa, where we continue to see strong growth and opportunity."
Over its 12 years operating in Nigeria, Uber had expanded its services. In the commercial hub of Lagos, it launched a boat service in 2019 in an effort to help commuters bypass the city's notorious congestion.
Lagos, one of Africa's largest and busiest cities, is infamous for its long traffic jams that cause gridlock and hamper business activity.
Other ride-hailing taxi apps have launched in the West African nation over the last decade, including international competitors such as Bolt and inDrive, as well as a number of local operators.
But the Nigerian market has become increasingly challenging for them all, with drivers staging protests and industrial action in recent years over rising operating costs, low fares and working conditions.
The removal of Nigeria's fuel subsidy after President Bola Tinubu's election in 2023 saw the cost of living rise. The subsidy had kept down the price of petroleum products low for decades.
This year, motorists have been hit again by the rise in petrol prices following the US's war with Iran.
Uganda's Daily Monitor newspaper said Uber's departure would mean a major change for commuters in the capital, Kampala. But it said the void was likely to be filled by other taxi apps such as Faras, Bolt and SafeBoda.
Uber pledged to support employees and drivers affected by the decision and said its help centre would remain open for those in Nigeria and Uganda until 23 September to deal with outstanding issues.
