Former Watford midfielder Chez Isaac put the hosts in front early on, but Naylor headed the Exiles to a replay, which will take place at Rodney Parade on November 19.
Braintree got off to the perfect start after eight minutes when Isaac latched on to captain Kenny Davis' lofted through ball - he took one touch before volleying home low into keeper Lenny Pidgeley's far corner.
Only a deflection stopped Braintree taking a 2-0 lead moments later when Dan Holman let fly from outside the box.
Davis then shot straight at Pidgeley before County's solitary effort of the first half, fired in by Michael Flynn, flew wide of keeper Nick Hamann's left-hand post.
The visitors did draw level five minutes after the break though when Naylor headed in Adam Chapman's cross.
Justin Edinburgh's side then hit the woodwork twice in two minutes, first through Christian Jolley, who fired his shot against the post and then Flynn, who clipped the crossbar from close range.
Isaac almost snatched a winner for the Brains, but Pidgeley denied his stinging effort before Flynn and substitute Conor Washington also tested Hamann's reflexes.