A strike on the same base in April 2018 left two peacekeepers dead and several others wounded.
Mahamat Saleh Annadif, the UN's special representative for Mali, said: "Peacekeepers of the MINUSMA force at Aguelhok fought off a sophisticated attack by assailants who arrived on several armed vehicles.
Some 13,000 peacekeepers are deployed in Mali as part of a UN mission. It was deployed in 2013 after Islamist militias seized the north of the country in 2012. They were eventually pushed back in 2013.
"The attack demands a robust, immediate and concerted response from all forces to destroy the peril of terrorism in the Sahel," added Annadif.
A peace agreement signed in 2015 was aimed at restoring stability.
But the accord between the government and armed groups has failed to stop violence by Islamist militants who have also staged attacks in neighbouring Burkina Faso and Niger.