The injury-hit Super Eagles needed a close-range header from star striker Victor Osimhen before half-time to secure a share of the spoils in the second game in Group A, the Napoli marksman answering back within two minutes of a shock Equatorial Guinea opener netted coolly into the bottom corner by Polish-based forward Iban Salvador Edu.
However, Osimhen also spurned a few other opportunities on the day including a golden chance after the interval as Nigeria piled on the pressure but failed to find another way past impressive Alaves goalkeeper Jesus Owono.
Osimhen was sent through with just under 15 minutes to play at the Alassane Ouattara Stadium - AKA the Olympic Stadium of Ebimpe - but dragged a right-footed shot comfortably wide of the near post in horrible fashion. It was a chance that the recently-crowned African Football of the Year would usually take with minimal fuss.
Instead it rather compounded another disappointing AFCON afternoon for Nigeria, who won the last of their three continental titles a decade ago and were dumped out of the tournament in the round of 16 in Cameroon in 2021.
They will have to improve sharply for Thursday night's high-profile showdown with Ivory Coast, with the hosts having opened proceedings with a comfortable win over Guinea-Bissau on Saturday.
For Equatorial Guinea, their reputation as a force to be reckoned with at AFCON remains. Though appearing at the competition for just the fourth time in their history this month, they finished fourth in 2015 and reached the quarter-finals on both other occasions, stunning defending champions Algeria last time around.
A hard-fought opening draw against one of the tournament favourites and traditional African football powerhouses is a fine result before they take on minnows Guinea-Bissau later this week.
Nigeria head coach Jose Peseiro could come under fire for his team selection, choosing to bench the likes of AC Milan attacker Samuel Chukwueze and Fulham defender Calvin Bassey after a flat warm-up defeat by Guinea in Abu Dhabi on Monday and back-to-back World Cup qualifying draws against Zimbabwe and Lesotho.
Instead he put his faith in the likes of William Troost-Ekong and Moses Simon, with Royal Antwerp's Alhassan Yusuf making his senior international debut in midfield in the absence of Wilfred Ndidi and home-based goalkeeper Stanley Nwabili handed his first competitive start between the posts.
Nigeria are also without the likes of in-form Bayer Leverkusen forward Victor Boniface, Nottingham Forest's Taiwo Awoniyi and Real Sociedad striker Umar Sadiq as the injuries piled up before AFCON once again, while late call-up Terem Moffi played for Nice on Saturday night and Yusuf was stretchered off on Sunday to mar an otherwise excellent debut.
The absences of the likes of Boniface, Awoniyi and Sadiq pile more pressure on attacking talisman Osimhen, whose movement was sharp as he was put through a few times but mostly denied by a combination of Owono and the offside flag.
Simon's low strike was touched onto the post by Owono just before the interval, while left-back Zaidu Sanusi also wasted two glorious opportunities on a frustrating day for the Super Eagles.