A controversial Ricardo Rodriguez penalty in the first leg ultimately proved the difference between the two sides in the end, leaving a bitter taste in O'Neill's mouth as Norn Iron's wait for a fourth World Cup finals appearance goes on.
This will be Switzerland's 11th qualification to the FIFA World Cup after making their debut at the second edition in Italy in 1934.
Petkovic said he was proud of his players although he was not so happy when misfiring forward Haris Seferovic was jeered off the field by a section of the home crowd.
"We will take it match by match, opponent by opponent and we're not setting any limits".
Twitter user James Lorenzo created a "supercut" from just the final 20 minutes of the second leg to give you an idea as to what you missed. Tonight we played with raw courage.
"We are a good team, I think we are a better team than Northern Ireland, and tomorrow with all the fans and all the support we have here, we want to make them proud and we want to qualify for Russian Federation".More news: AT&T CEO: I 'Have No Intention' of Selling CNN
But the longer the game went on at 0-0, the more empowered Northern Ireland were.
Seferovic glanced a free header wide and shot wide of the near post as the Swiss began to take control.
So who gets to start on this vital night?
Michaeol O'Neill threw on Jordan Jones and Josh Magennis, hoping one of them could spark something in the final third.
Northern Ireland came within inches of forcing extra time in injury time at the end of the tie, only for West Brom defender Jonny Evans to see his header hacked off the line by Rodriguez.
Rodriguez moved across the goalmouth toward the post and hooked the ball clear as he fell backward into the goal.