Enugu Rangers were eliminated from the CAF Champions League after losing 3-1 away to Angolan club Sagrada Esperanca on Sunday, leaving Nigeria with no representative in the group stage.
Rangers went out 3-2 on aggregate after building a one-goal lead in the first leg of the second round qualifier last weekend.
The Nigerians have competed in the Champions League four times and never made it to the mini-league phase, where prize money kicks in with $800,000 (715,000 euros) for qualifiers this season.
Enugu trailed 2-0 during the first half in Luanda against rivals playing 850 kilometres (530 miles) from their Dundo base because the ground there does not meet international standards.
Anayor Ogbonna then netted before half-time for Rangers, bringing the clubs level on aggregate at 2-2, but edging Enugu ahead on away goals.
Jaime Pimpao scored the only goal of the second half on 67 minutes to put Sagrada two goals ahead again in the second leg, and they retained that advantage to seal the fate of Enugu.
The other Nigerian qualifiers for the premier African club competition this season, Remo Stars, lost to Moroccan side FAR Rabat in the first round last month.
Sagrada reached the group stage once in three previous appearances and their qualification comes after the surprise failure of fellow Angolans Petro Luanda to be among the 16 survivors.
Petro were held 0-0 at home by Maniema Union from the Democratic Republic of Congo on Saturday and lost 2-1 on aggregate.
Malian club Djoliba created history after winning 1-0 away to Togolese outfit ASKO Kara in Lome and progressing 2-0 on aggregate.
At the 12th attempt, the Bamako team became the first club from the west African nation to reach the group phase of the Champions League.
Former champions Stade Abidjan of the Ivory Coast, back in the competition after a 54-year absence, FAR Rabat and Al Hilal of Sudan also qualified on Sunday.