The home sides lead was doubled just seven minutes later as Matt Bodkin raced down the left before cutting in and finely curling his effort far corner to gibe Margate a 2-0 lead.
That was how it stayed until the 55th minute as Byron Lawrence curled in a spectacular free kick from 25 yards to reduce the arrears.
Leiston were growing in confidence and Matthew Blake wasted a glorious chance before the excellent Tom Wynter intercepting at the crucial moment to keep the Gate’s slender lead.
Margate suffered heart ache in the 91st minute as a free kick was swung inwards which found its way to substitute Joe Marsden at the far post who nodded past Pidgeley despite the home oppositions cries for offside.
The draw means both teams remain unbeaten after three games in the Bostik Premier with Leiston on seven points and Margate on five from a possible nine.