Super Eagles striker Stephen Odey got a consolation goal for Zurich in the fourth minute of stoppage time of the 3-1 loss to Basel.
Switzerland U19 international of Nigerian Descent Noah Okafor was on target as FC Basel qualified for the final of the Schweizer Pokal by beating FC Zurich 3-1.
The versatile winger needed only five minutes to open the scoring when his brilliant swerving shot from just outside the box beat the goalkeeper.
Okafor was replaced by Edon Zhegrova moments before the end of the game while Odey featured for the entire duration of the match and was cautioned in the 82nd minute.
The Nigeria strikers will be looking to continue the impressive forms in the second leg at St. Jakob-Park on May 4.
Both players will hope to make the Super Eagles squad to the 2019 Africa Cup of Nations in Egypt in the summer.
Nigeria are in Group B along with Burundi, Guinea and Madagascar.
