The Super Eagles got off to a perfect start with defender & Coca-Cola man of the match William Troost-Ekong scoring his first international goal in the 14th minute, but a rash challenge from second-half substitute Ola Aina paved the way for a comeback from their adventurous visitors, as Ben Malango netted the equaliser from the penalty spot.
Gernot Rohr handed debuts to Simeon Nwankwo and Junior Lokosa, with Kelechi Iheanacho completing a three-man attack. While Oghenekaro Etebo and Elderson Echiejile returned to the side and Tyronne Ebuehi continued in the right-back position.
For Congo, Florent Ibenge had Benik Afobe lead the line, with Paul-José M'Poku providing support for the Bournemouth striker.
In an opening exchange that saw the hosts dominate proceedings, the first chance of the game fell to Nwankwo, who hit the post with a ferocious left-footed effort after showing impressive skill to get past a Congo defender. Iheanacho's effort from the rebound was blocked.
However, in the eighth minute, the Super Eagles were tested but goalkeeper Francis Uzoho's reactionary save prevented Afobe from breaking the deadlock.
Six minutes later, Nigeria opened the scoring through Troost-Ekong, off a routine free-kick.
Etebo, standing over the setpiece, and Iheancho combined well to con the Congolese defence with the Bursaspor defender adding the finishing touch.
Afterwards, the visitors enjoyed more possession, camping Rohr's men - who mostly played on the break - in their half.
Afobe almost levelled proceedings but saw his shot flash wide off the target in what was the last meaningful action of the opening 45 minutes.
After the break, it took some while for the game to get going as, again, a touch from Nwankwo sparked it to life. The lanky marksman displayed his aerial prowess after he connected perfectly to a long throw from Aina but saw his header thwarted by Leopards goalkeeper Anthony Mossi.
Ten minutes later, the Crotone striker almost helped Nigeria get a second after piling pressure on Mossi but Etebo’s curled effort missed the unguarded net.
But with 12 minutes left, Afobe’s replacement Malango got the equaliser for the visitors from the spot after Aina was penalised for bringing down a marauding Issama Mpeko.
Immediately, Iwobi sought to find a response but his effort went whiskers away from the bottom corner, and the Rohr's side had to settle for a share of the spoils.
Nigeria play England at Wembley next, but before the tie, five players are expected to be dropped from the 30-man provisional list for the World Cup.