Defender Przemysław Wiśniewski struck from long range in the fifth minute of added time to rescue a result for the hosts in their final match before this autumn's UEFA Nations League fixtures.
Nigeria took the lead in the 23rd minute through Terem Moffi, who finished off a counterattack. The goal was initially ruled out for offside but was awarded following a VAR review.
Poland equalised just before halftime when 18-year-old defender Kacper Potulski scored his first international goal after a low cross from Nicola Zalewski.
Potulski, making his first appearance for the national team, became one of the youngest scorers in Poland's history.
The visitors regained the lead in the second half. Paul Onuachu converted a penalty after a VAR review determined that Poland midfielder Kacper Kozłowski had touched the ball with his arm inside the area.
Poland pushed for an equaliser, with captain Robert Lewandowski twice denied by Nigeria goalkeeper Maduka Okoye.
The Barcelona striker first failed to capitalise on a defensive error before Okoye produced a double save from Lewandowski and Jan Bednarek.
With defeat looming, Wiśniewski unleashed a powerful shot from outside the box in the final seconds of the match to level the score.
Nigeria had several opportunities to extend its advantage, including a close-range header from Onuachu that went narrowly wide shortly after halftime.
Wednesday's match was part of Poland's preparations for upcoming Nations League games against Bosnia and Herzegovina, Sweden and Romania.
Poland and Nigeria had met only once before. They played a friendly in Wrocław, southwestern Poland in 2018, when Nigeria won 1-0 thanks to a penalty from Victor Moses.
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Source: TVP, IAR, PAP