O'Neill was left to lament some soft defending as a defensive mix-up allowed Amiri to pounce for Germany's second, whilst he also questioned the awarding of the free-kick which Wirtz superbly dispatched.
"For 60 or 65 minutes we were well in the game. The second goal is a bit of a freak goal, we could have defended it better. The third goal isn't a free-kick. It's a fantastic finish but it's a soft free-kick," he explained.
"I thought the referee was a bit fussy in the second half. He refereed it well in the first.
"We were well in the game and needed to get to that final 15 minutes and we might have had a final chance, but the game drifted away from us."
Northern Ireland sit second in Group A following a win and a defeat from their opening two games.
O'Neill believes his side are where they expected to be at this stage of qualifying, with two huge home games against Slovakia and Germany to come in October.
"It's tough to play two games away from home," he said. "We got what we hoped for, but we're a bit disappointed it's not a little bit more.
"We have to be ready to play back-to-back at home and we know two good results will put us in a good position."