O'Neill's bold team selection, which featured four changes and Stuart Dallas despite an injury concern, was reminiscent of the way he shuffled his pack against Ukraine at Euro 2016 when Northern Ireland were facing elimination after a poor performance against Poland.
Northern Ireland had very few chances to score, with both of their decent ones coming at either end of the match. We should leave this discussion apart.
O'Neill shared tearful embraces with some of his players at the final whistle, and a long hug with Switzerland coach Vladimir Petkovic.
A chilly, rain-soaked evening seemed ideal for the visitors to rise to the atmosphere created by their noisy fans.
With their spot in Russian Federation secured, the 11th-ranked Swiss will be in the pot of second-seeded teams for the World Cup draw on December 1 in Moscow.
Things were much the same in the second half, though Northern Ireland did appear a slightly more purposeful in attack, with Conor Washington and George Saville squandering opportunities. That said, Switzerland were the better side by a considerable distance and it's hard to see how Michael O'Neill can turn this in his team's favour.
The urgency of the opening half hour in Basel, on a sodden surface that soon cut up, defied the often laborious first leg.
Within 30 seconds of the restart, Shaqiri nearly curled a patented left-foot strike under the crossbar after Brunt had failed to deal with Rodriguez's deep cross. He tried to force Switzerland back and Chris Brunt tested Yann Sommer with two rockets from 30-yards.
But, the home side dug deep and held on to the draw they needed, denying a Northern Ireland side who are likely to once again highlight the impact of Rodriguez's controversial penalty in Belfast.
Chris Brunt anxious the hosts first, forcing Yann Sommer into a flying save to keep a stunning 30-yard drive out of the top-right corner, before Seferovic inexplicably failed to direct Shaqiri's pinpoint cross beyond Michael McGovern with a glancing header.