Northern Ireland were minutes away from securing a famous win in Porto thanks to a maiden international goal from Niall McGinn after 30 minutes.
A late equaliser from Helder Postiga earned Portugal a 1-1 draw despite some heroic Irish defending in the closing stages.
O'Neill told Sky Sports News that the performance epitomised the belief his team have in their ability to grind out results against bigger nations.
He said: "Our players were just magnificent, the work rate and desire and how they worked for each other, you can't ask for any more than that.
"At times I thought we passed the ball really well and I'm coming away disappointed with just a draw.
"We have to take confidence and belief from what we did tonight, our togetherness and spirit is unquestionable."
Northern Ireland can now look forward to four successive home qualifiers as they look to move up the table in a difficult World Cup qualifying group featuring Portugal, Russia and Israel.