A first-half double from Galatasaray striker Victor Osimhen sent the Super Eagles soaring past the Wasps at Amahoro Stadium in Kigali.
Before the match, the East Africans were top of Group C, but the recent defeat has seen them slip to third place, behind South Africa and Benin Republic.
While reflecting on where his team went wrong against the three-time African champions, the experienced defender is confident that his side will bounce back and do whatever it takes to progress.
"We are disappointed by the defeat to Nigeria because it does not truly reflect how we played," Omborenga told Flashscore.
"We approached the match with the ambition to win and stay at the top of the group, but unfortunately, we ended up losing.
"The first-half goals scored by the Nigerians unsettled us, and we struggled a bit in the second half. Our fans are disappointed with the result.
"We’ve managed to learn some important lessons that will help us in the upcoming qualification matches."
Adel Amrouche’s men now walk a tightrope in their bid to achieve their World Cup dreams. However, the APR star believes that all hope is not lost just yet.
He continued: "Losing a game does not mean our race to qualify for our first World Cup is over. Other countries in Group C have also lost a game or two.
"I think it's still early to rule us out because the qualifiers are a marathon, not a sprint. We've been labeled as underdogs, and that alone brings out the best in us.
"Our coach (Amrouche) did not hide his disappointment with the result, but we've moved on, and our focus is now on our next game on Tuesday."
Rwanda will look to bounce back to winning ways as they host Lesotho in Kigali. Similar to the Wasps, the Crocodiles suffered a 2-0 defeat to South Africa in their last match.
The score at Peter Mokaba Stadium was still 0-0 before Relebohile Mofokeng put Bafana Bafana ahead on the hour mark. Jayden Adams then netted the second just four minutes later.
Omborenga is optimistic that Rwanda can complete a double over Lesotho, having won the first leg 1-0 in Durban, though he stressed that they will not underestimate their opponents.
"Lesotho is not an easy team, but we have a slight advantage because we won the first match last year," he added.
"However, this game will be different as they will be looking for revenge – but we are ready for them. Our goal is to win, and we won’t underestimate them."
Lesotho coach Leslie Notsi had warned that his team would not be a pushover, despite their standing in African football.
"For us as Lesotho, the upcoming qualifiers are quite crucial for us. We need to secure points, we are playing two away matches which somehow makes it a little bit tight for us but at the same time, as we have been playing our matches away from home, so we are used to this scenario,” Notsi told the media.
“It's going to take a lot from us but we believe in ourselves that these are the games that we are always happy to play in terms of us as a small footballing country to improve our game and be a very competitive outfit.
"Yes, of course there are other countries that on paper are the favourites but then they still have to secure those points and qualify for the World Cup."
Lesotho are currently fifth in the group, having earned five points from five matches played so far. Their only victory was a 2-0 win over Zimbabwe in June 2024.
