The Saints were behind after just 13 seconds at the Britannia Stadium when a clearance from home goalkeeper Asmir Begovic was caught by a gust of wind and bounced over opposite number Artur Boruc.
However Mauricio Pochettino's high-flyers shook off the setback and drew level through striker Jay Rodriguez before half-time.
Southampton eventually earned a point to extend their unbeaten run to seven games, and Fonte felt his side showed commendable spirit in light of the unusual early goal.
"It was a very strange start to the game," said the defender. "We were in the huddle just before kick-off saying, 'Come on, if we can keep a clean sheet today...' and 30 seconds later we were losing 1-0.
"It was obviously a bit of a shock but I think we showed tremendous character. We did discuss before the game that we would play with the wind behind us if we won the toss.
"We are a little bit disappointed with some of the decisions, especially the handball near the end. We felt it was a clear penalty.
"Having said that we could have been in real trouble if Shawcross had scored just after their goal. It was a good chance.
"We got away with it, maybe we deserved that after their goal."