Africa's biggest economy was last in recession in 2016, its first in a generation, and emerged the following year.
But growth had been fragile and the coronavirus pandemic hit the economy hard, as did low oil prices. The continent's top oil exporter relies on crude sales for 90% of foreign exchange earnings.
"Q3 2020 Real GDP contracted for second consecutive quarter by -3.62%," Yemi Kale said on Twitter.
"Cumulative GDP for the first 9 months of 2020 therefore stood at -2.48%," he added.
The government had previously said it expected the economy to contract by as much as 8.9% this year in a worst-case scenario without stimulus.