It was late heartbreak for National League North pair Boston United and Gateshead.
Michael Brewster's goal for Atherton Colleries saw off the Pilgrims while Simeone Colborne came off the bench for Halesowen to halt the Heed's cup progress.
Braintree were in front after two minutes against Yate Town but conceded a late brace from Louis Britton while Wealdstone fought back against Royston through Ross Lafayette and Jerome Okimo, only to be thwarted six minutes from time.
Zak Lilly opened the scoring for AFC Telford as they made light work of Guiseley - Marcus Dinanga and an Aaron Williams double made it rout.
Chester became only the second team to win at Brackley since February - Anthony Dudley's second-half strike enough for the Blues.
Kettering avoided a banana skin at Peterborough Sports despite playing the final half an hour with ten men.
Daniel Nti added the gloss to their performance late on after Lindon Meikle and Aaron O'Connor got them up and running.
Maidstone and Dartford couldn't be separated in the Kent derby - two goals from Elliott Romain saw the Darts twice come from behind to force a replay.
Altrincham repeated their FA Cup win at Bootham Crescent. They even had the same scorer, Tom Peers, to settle things against York.
A Jack Barham hat-trick saw Dorking ease past Leatherhead while Southport survived a scare at Colne.
The Port found themselves two behind before Devarn Green, Bradley Bauress and David Morgan completed the turnaround.
Moses Emmanuel got a debut goal for Welling as they saw off National League South rivals St Albans.
Elsewhere, a quickfire Alfie Rutherford double late on helped Havant & Waterlooville past Cinderford.
Saturday's FA Trophy final scores in full:
Atherton 1-0 Boston United
Bath City 0-0 Gosport
Blyth Spartans 1-1 Alfreton
Brackley 0-1 Chester
Braintree Town 1-2 Yate Town
Chelmsford 2-1 Hungerford
Colne 2-3 Southport
Concord 0-0 Slough
Curzon Ashton 3-0 Kidderminster Harriers
Darlington 2-1 Gainsborough Trinity
Dulwich Hamlet 2-2 Chippenham Town
Eastbourne 3-1 Hartley Wintney
Guiseley 0-4 AFC Telford United
Halesowen 1-0 Gateshead
Haringey 1-4 Hemel Hempstead
Havant & Waterlooville 3-1 Cinderford
King's Lynn 0-0 Hereford
Leamington 2-1 Spennymoor
Leatherhead 0-3 Dorking Wanderers
Maidstone 2-2 Dartford
Oxford City 1-1 Hornchurch
Peterborough Sports 0-3 Kettering
Tonbridge Angels 2-1 Bognor Regis
Wealdstone 2-3 Royston
Welling 3-1 St Albans
Weymouth 1-0 Hastings
Workington 0-1 Farsley Celtic
York 0-1 Altrincham