After Odion Ighalo’s opener from the penalty spot was cancelled out by Rody Melanie following Francis Uzoho’s blunder, Henry Onyekuru and Moses Simon found the target to help the West Africans claim a win at the Stephen Keshi Stadium.
The victory ensured that the three-time African champions finish the qualifying campaign as Group E leaders with 13 points from six games.
However, the German tactician, who admitted their visitors made the game difficult for them, noted mistakes which must be improved on subsequently.
''We knew that it would be a difficult match because it was not the same team from Seychelles. They started preparations very early in March and seven new players were invited," Rohr told media.
'The players knew that we have to expect a difficult match, they only defended. It was attack, defense so we tried to come in from the wings.
''We scored the first goal through a penalty, then there was an individual mistake that can happen to anybody.
''In the second half, we scored two nice goals. They did the job, we wanted to win the game and finish top of the table which is very important for the Fifa ranking and be the head of the group at the Afcon.
''A lot of mistakes still in the construction of the game we have to improve, I could see some interesting players. It was good to see everybody again after four months.''
Next up for the Super Eagles is a friendly game against Egypt on Tuesday at the Stephen Keshi Stadium.