The Gills keeper was beaten by Tom Pope and Lee Hughes before Danny Kedwell pulled back what proved to be nothing more than consolation at Priestfield.
Vale's victory saw them leapfrog the Gills at the top of the League Two table although the Kent club still boast a game in hand.
Yet Nelson insists the fixture will not define Gillingham's season.
"It was no different to any other game for us, you (the media) might have been billing it up but we weren't. We were just getting on with it and we go out to win every game whether it be a team at the bottom or at the top," Nelson told Gillingham's official website.
"Yes it was a big game but we still have a game in hand and, on paper, if we win it we'll go back above them. It's not a massive loss; it may have been built up as the game of the season because it was two good teams going in to battle.
"It's how we bounce back, we can't affect those three points now. They're gone so there's no point worrying about them, we're in a great position, we've got ourselves in this position and no-one is panicking downstairs.
"We don't over celebrate when we win and we don't hang ourselves when we don't. That's been the message all season, we have had setbacks but we have always bounced back."