Ricardo Rodriguez's controversial penalty has the Swiss in pole position to win the play-off and reach Russia, with Northern Ireland needing to overturn a 1-0 deficit on Sunday to qualify for the tournament for the first time since 1986.
The AC Milan left-back converted from the spot after referee Ovidiu Hategan had judged Corry Evans had blocked Xherdan Shaqiri's volley with a hand, even though the ball appeared to strike the midfielder on the back as he turned away from the shot.
O'Neill branded the decision in the immediate aftermath as "staggering", although he now hopes the disappointment can work in his squad's favour in Basle.
"There was a lot of emotion after the game. It's gone now," he told the media.
"We will take motivation from it and we are focused on the result.
"I think we have to be better in possession. We know we can play better and the fact the score is 1-0, that means there is all to play for."
Captain Steven Davis echoed his manager's rousing words - and urged his team-mates to remain positive as they aim to avoid falling at the final hurdle in qualifying.
"We have all dreamed of getting to a World Cup and we are 90 minutes away from that. We have to give it our all," the Southampton midfielder said.
"Any frustration from the other night is fuel for us. We have nothing to lose. We have to use that to our advantage.
"We have to be braver in possession and without [the ball]. A lot can happen in 90 minutes."
O'Neill will be without Corry Evans, who is suspended after picking up a booking in the penalty incident in Belfast, while Stuart Dallas will hope to recover from a bruised foot in time to feature.