The Ducks started the brighter of the two sides with Steve Clark twice coming close to opening the scoring in the first five minutes.
Thame's Wayne Cort had a goal disallowed for a push on Daniel Gordon on 24 minutes and just as Thame were coming into the game Aylesbury took the lead.
On his return to his former club Greg Williams saw his cross find the head of Chris Boothe who in turn marshalled the ball across the face of the goal for Steve Clark to hammer home with a shot that left Thame keeper Alan Foster totally flat footed.
Thame introduced ex-Duck Jefferson Louis at half time and the majority of the second half was played with Aylesbury on the back foot.
Mark West saw his shot well saved by Adam Wheeler on 51 minutes before Rob Paris blocked a goul bound shot from Chris Potter.
With 7 minutes remaining a slick passing movement involving 4 Thame players saw Wheeler deny West once again.
Aylesbury had a chance to double their lead deep into injury time as Stuart Maynard's free kick was acrobatically met by Ollie Stanbridge, however the visitors had to be content with a single goal victory as the ball was superbly tipped over the bar by Foster.