Braintree took the lead on 15 minutes when the Ducks failed to clear a throw and Mark Jones beat Chris Day from 18 yards.
The Ducks pushed hard for an equaliser with Craig Maskell, Kezie Ibe and Gareth Risbridger all going close before Tommy Noble scored Braintree's second goal on 76 minutes following a mistake by Aylesbury debutant Alex Stanley.
With 8 minutes to go substitute Chris Bangura volleyed home from 6 yards out to give Aylesbury hope before Craig Maskell won and scored a penalty with 4 minutes left and secured what had looked like an unlikely point.
Braintree Town
Aylesbury United
Bedford Town
Heybridge Swifts
Billericay Town
Enfield
Bishop's Stortford
St. Albans City
Chesham United
Ford United
Hampton & Richmond Borough
Aldershot Town
Harrow Borough
Grays Athletic
Hayes
Basingstoke Town
Maidenhead United
Kingstonian
Purfleet
Hitchin Town
Sutton United
Hendon