The Flying Eagles, 1-0 winners from the first leg in Bujumbura last month survived early onslaughts from the visitors in a first half that produced no goal.
Captain Kelechi Nwakali scored the second goal nine minutes later when he drove home a free kick from 23-yards.
The Burundians pulled one back three minutes from time through Magloire Ndikumana who cashed in on laxity in the Flying Eagles defence to make hay, but the Flying Eagles held on to claim a vital victory and set up a date with Sudan at the final round.
Nigeria coach Emmanuel Amuneke described the back-to-back victories over Burundi as a confident booster ahead of the final round meeting with Sudan.
“It was not an easy game because Burundi came with a game plan but we were able to contain them especially in the second half. The win is good for the confidence of the boys and we would continue to work hard in the coming days for our next matches against Sudan in order to qualify for the U-20 AFCON in Zambia next year,” noted Amuneke.
Elsewhere in Dakar, Aliou Badji struck twice in the second half to aid Senegal to a 2-0 win over Tunisia and 4-1 on aggregate.
Angola sealed the place at the ultimate round despite suffering a lone goal defeat away to Gabon in Libreville. Junior Mboulou Nzigou scored the only goal two minutes from time as the ‘Palanquinhas’ advanced 3-1 on aggregate.
Earlier on Friday, Egypt saw off Rwanda 3-2 on penalties in Cairo after a 1-0 win by the visitors took the tie to kicks from the short distance.
Seven teams will emerge from the qualifiers to join host Zambia for the final tournament of the 20th edition of U-20 Africa Cup of Nations scheduled for 26 February to 12 March 2017.
Friday, 10 June 2016
Egypt 0-1 (3-2pen) Rwanda (1-0)
Saturday, 11 June 2016
Senegal 2-0 Tunisia (2-1)
Nigeria 2-1 Burundi (1-0)
Gabon 1-0 Angola (0-3)
South Africa 2-0 Namibia (0-0)
Sunday, 12 June 2016
Ghana vs Ethiopia (1-2)
Morocco vs Gambia (0-1)
Guinea vs Conakry (2-1)
Congo vs Burkina Faso (1-1)
Mali vs Mauritania (3-0)
Lesotho vs Mozambique (1-1)
Cameroon vs Zimbabwe (0-0)