Despite being without a number of regulars through injury, Joachim Low's squad secured a place at the 2018 World Cup with an impressive 3-1 triumph over their nearest rivals in Belfast.
The hosts conceded twice inside 21 minutes and were fortunate to only be 2-0 down at half-time, goalkeeper Michael McGovern and the woodwork both denying Germany.
However, a change of shape at the break saw an improved second-half display from Northern Ireland and although Joshua Kimmich volleyed in a late third for Germany, Josh Magennis rewarded the vocal home support with a consolation goal in injury time.
"The early goal made it difficult, it knocked us back and took us a while to get going," O'Neill told Sky Sports.
"We got up to the ball better in the second half. If that was because of the change of shape, then that is my fault. Through players like Toni Kroos and Mats Hummels, it is difficult to get a touch on the ball.
"You are not going to get too many chances against Germany. You want them to miss and then net the ones we get.
"This was a bonus game for us, it could have gone to 4-0 or 5-0 but we kept our goal difference in a healthy state. It could easily have been obliterated."
Northern Ireland have little time to lick their wounds - they complete their campaign with a crucial trip to Norway on Sunday.
O'Neill's squad, who have 19 points from nine games, are still not certain of a place in November's play-offs, as only the eight best runners-up go forward to the next stage of qualifying.