John Pemberton saw his team fight back from 3-0 down to draw themselves level with Chesterfield in the closing stages.
But then goalkeeper Callum Burton was red carded - and Ebbsfleet had a match-winning penalty.
Michael Cheek had the task of putting the ball beyond defender Will Evans who had taken the gloves but the man who scored the goal to make it 3-3 saved the day.
His 99th minute spot-kick stop was big news for a club who hope to announce their new manager in the coming week.
“It was astonishing,” said a the stand in. “Nobody was expecting what happened.
“The response from the players in the second half was absolutely unbelievable - they showed incredible spirit.
“We cleared the air at half-time but the second half was a little bit special.
“They played with no fear and Will came up with the goods. It’s a game of football few people will forget.”