More than 5,000 Nigerians are believed to reside in Sudan, many of them students.
Nigerian commercial carrier Air Peace landed in capital Abuja around 11:40 pm with 260 passengers while a Nigerian Air plane arrived a few minutes later with about 90 passengers, AFP reporters saw.
The visibly happy returnees were recieved by the foreign ministry and emergency services.
The fighting in Sudan has killed at least 550 people, displaced tens of thousands and triggered an exodus of foreigners and international staff.
The Nigerian planes had left Aswan in neighbouring Egypt for the five-hour journey to Abuja after several days of delay at the border.
An initial convoy of 13 buses left Sudan’s capital Khartoum on Thursday for Egypt with a plan to fly to Nigeria on Friday, but the group was refused permission to cross the frontier.
Egyptian authorities on Monday agreed to let them cross after Nigerian President Muhammadu Buhari intervened, according to the Nigerians in Diaspora Commission.
Another 20 buses prepared to evacuate hundreds more Nigerians still blocked in Sudan.
That convoy would no longer travel to Egypt, but to Port Sudan, a city on the Red Sea 675 kilometres (420 miles) from Khartoum, from where they should then fly back to Nigeria, a National Emergency Management Agency spokesperson told AFP.
Battles have raged in Sudan since April 15 when conflict erupted between the country’s de facto leader Abdel Fattah al-Burhan, who commands the regular army, and his deputy-turned-rival Mohamed Hamdan Daglo, who commands the paramilitary Rapid Support Forces (RSF).
After both sides agreed to extend a three-day ceasefire, air raids, shooting and explosions shook Khartoum, the capital, again on Monday.