However, the decision stood and Ricardo Rodriguez scored from the resulting spot-kick to give the Swiss a crucial away goal heading into the second leg on Sunday.
Switzerland were the better team but they owe their slender lead largely thanks to an alarmingly incompetent piece of officiating from Romanian referee Ovidiu Hategan that Michael O'Neill called the worst he had ever seen in global football and saw the biggest night of football in Belfast for 36 years descend into acrimony.
ADIDAS have released their new kit designs for the 2018 World Cup.
"I don't have to pick them up", says O'Neill defiantly.
"I've analysed the match again and there were decisions that went against us, especially in the 85th minute".
"The lads said to keep my chin up; these things happen in football but the referee didn't help us at all tonight".More news: CWI strikes five-year tour agreement with Pakistan
"I didn't know. The other players appealed, but it was hard to see what happened, I tried to shoot and someone was in front of me".
While Northern Ireland were aggrieved, Shaqiri said he felt his side had dominated and deserved their lead.
Indeed, the hosts did not register a shot on target and Haris Seferovic and Shaqiri both came close before the penalty was awarded. I know it him me on the back of the shoulder and I'm just absolutely gutted.
"We go into the second leg with the strongest team we have available and I think we showed enough in the second half to show we can get something".
No European team has ever qualified for the World Cup via the play-offs after losing the opening leg at home, highlighting the magnitude of the task awaiting the Northern Irish in Basel. And to actually think Northern Ireland has probably homed one of his smelly relatives! Switzerland enjoyed much more room in the closing stages of the first leg, and they will need to exploit that much better in the next meeting.
The defeat leaves Michael O'Neill's side with something of a mountain to climb on Sunday night, as they look to qualify for their second major finals in succession. "They have to be play more offensively".