Emley are the last remaining team from level nine of the football pyramid, having celebrated successive cup wins over Northern Premier West sides, in Widnes and Mossley, and they created the best chance of the opening stages when Ruben Jerome's shot was saved by the keeper.
At the other end, it was Dec Lambton who had to make a save from a long distance curling shot.
Mossley pressure late in the first half looked to have paid off when they were awarded a penalty but Lambton dived low to his left and produced a wonderful save to keep the sides on level terms at the break.
Jake Kelly replaced Jack Cowgill for Emley at half time and it was the Pewits who were on the front foot early in the second half, Walker firing a low shot that the Mossley keeper saved.
James Walshaw replaced Jerome as Emley looked to take control, and they almost did when a great move down the right saw the ball flashed across the area but Paul Walker was unable to control the ball cleanly and his shot went over.
With less than two minutes left, Emley looked to have won it when they broke the deadlock through Walker but that wasn't the end.
Gooden had a sight of goal to try and wrap the tie up but he blazed high and wide and within a minute, Emley's hearts were broken when Oumar Camara pounced to score a dramatic equaliser.
Mossley almost snatched a winner with their next attack but they couldn't convert from a corner, and with almost the last action of the 90 minutes, Lambton pulled off another great save to keep Emley in the tie.
Despite conceding so late, the home side showed great character in extra time and they regained the lead when Ross Hardaker’s cross was fumbled by the keeper and the referee ruled the ball had crossed the line.
Mossley piled bodies forward but Emley's rear guard, led superbly by skipper Knowles and Pashley, stood firm.
And Emley then grabbed the goal that secured their place in the third qualifying round. Joe Kenny set the attack in motion, Gooden carried it on and a lovely dinked ball into the danger zone saw James Walshaw nod home after the visitors failed to clear.
Emley are in cup action again on Saturday when they visit Brigg Town in the FA Vase second qualifying round.