The Super Eagles failed to break their World Cup opening game jinx with an own goal from Oghenekaro Etebo and a Luka Modric penalty, both coming off mistakes from corner kicks, condemning them to a 2-0 defeat at the Kaliningrad Stadium.
The west African side have now failed to win their first games at the quadrennial tourney since the 1998 edition when they won Spain 3-1. Also, the goals conceded were the third and fourth off corner kick situations in their previous three encounters.
Rohr's choice of tactics was questioned by fans and pundit alike . But the German handler has defended the urge not to revert to a back-three, stating they did well in countering Zlatko Dalic's approach and, however, only missed being 'professional' from set-piece situations.
"I think the organisation was okay. We didn't concede from normal play, we conceded from set-pieces," Rohr said after the game.
"Our system was okay. We cannot play with three when there is only one centre-forward, so we played with four because Croatia had three strikers. What we were missing today was to be more professional on set-pieces. Each game is different, we will see for the next game. We know we can play with three centre-backs but today was not that day.
Rohr also jumped to the defence of team captain John Obi Mikel - subbed off in the closing stages of the game after failing to exert his influence, and particularly failing to link effectively with striker Odion Ighalo.
"We play all the time with Mikel in this role of offensive midfield. It's was going well, we qualified and the team built behind them.
"I know he plays before in defensive midfield, in China he plays offensive and defensive. When we don't have the ball, everyone is defensive. Obi Mikel tried his best, it's not easy when you have to play against Modric and Rakitic when you see the clubs where they play and then the clubs where our players play.
On Alex Iwobi, he said: "Iwobi deserved to start the game, he had big work to do defensively against the right-back, he did it well, he had to work a lot, perhaps he was missing the energy for his offensive game.
"He did well, it was not his fault we lost the game."
Rohr still harbours hope that Nigeria can qualify from Group D, believing his side can muster four points off Iceland and Argentina - who played a 1-1 draw at the Spartak Stadium, earlier on Saturday .
"It's important to make at least four points to qualify. All is in our hands. Let's be positive and believe we can do it.
"We have the youngest team at the World Cup. Let them learn from this match and do better. We saw Iceland they are a strong team and they can do very well, but we know we can also do better."
Nigeria, rooted to the bottom of Group D with no point, face World Cup debutant Iceland on June 22.