The Flying Eagles on Sunday evening lost to Saudi Arabia ahead of their trip to Poland for the FIFA U20 World Cup.
The international friendly staged at the Sportschule Lindabrun ended goalless in the first half.
But the Saudi Arabians were on the front foot and were unlucky not to take the lead.
Ten minutes into the second half, Al Qadisiyah FC striker Khalid Al-Ghannam earned Saudi Arabia the lead but Swedish-based midfielder Henry Offia restored parity for the Flying Eagles nine minutes later.
Hamed Alghamdi scored what proved to be the winning goal with 12 minutes left on the clock.
Nigeria have lined up three more friendlies against TSG Hoffenheim (May 7/8), Red Bull Salzburg (May 14) and Red Bull Leipzig (May 17).
The Paul Aigbogun-led side are in Group D of the FIFA U20 World Cup, with their first match against Qatar on May 24, the United States on May 27 and Ukraine on May 30.
Players and officials of the Flying Eagles will spend the night in Vienna and will return to their hotel in Bad Gögging, Germany on Monday.