England were indebted to a dominant display before the break as goals from Gary Cahill and Harry Kane secured a 2-1 win over the Super Eagles on Saturday.
But the visitors matched England's formation after the break and quickly capitalised on the home side's failure to respond, with Alex Iwobi halving the deficit.
Southgate's side eventually got a foothold back in the game and the manager felt the outing provided valuable experience for his squad.
"I think we played really well with the ball especially, created a lot of good chances, far more good situations than we've had in recent games," Southgate told ITV.
"We were deservedly a couple of goals to the good at half-time. In the period leading up to their goal they changed their system and it took us a little while to figure out how to deal with that.
"What that did mean is that there was a little lift in the game that we had to cope with and manage, and that was a decent exercise for us to adjust to that."
After a week of being in the headlines for his tattoo and late arrival at the team's training camp, Raheem Sterling produced a lively display in which he was also booked for diving.
Southgate was content with the Manchester City star's contribution, as well as the attacking intent from the rest of the forwards in action.
"He played well," said Southgate. "The front four, some of the movement and interplay, we looked a threat with plenty of pace. Dele [Alli] and Jesse [Lingard] made unselfish runs.
"Some slightly better decision-making or quality in the final third and we would have scored more."