Neil Aspin admitted he thought his FC Halifax Town side were on their way to the last eight before they slip let a 2-0 half-time lead.
The two Conference Premier sides will fight it out in a third-round replay at The Shay tomorrow after Dartford launched a dramatic second-half fightback.
Aspin said: “I would have expected, after being 2-0 up at half-time, to get through to the next round.
“But you know that if you’re 2-0 up and you concede early on (in the second half) then it makes it a totally different game and, unfortunately, that early goal we conceded in the second half set the tone for the play.
“They made it very difficult for us, put a lot of balls into the box and at the end you have to hold your hands up and say it was a game of two halves.”
Richard Peniket followed up his hat-trick in the last round against Alfreton with an early goal when he touched in Paul Marshall’s superb free-kick.
Matt Pearson’s goal just before half-time looked to have sealed the win when he nodded in from Adam Smith’s cross.
But Dartford capped a strong start to the second half as Lee Burns headed in a corner before the hosts started pinning Halifax back.
Rory McAuley then converted one of the barrage of crosses in the final stages of a dramatic conclusion.
Dartford had a ‘goal’ disallowed deep into stoppage time and Peniket just failed to reach substitute Will Hatfield’s cross to seal it for the Shaymen.
Dartford: Brown, Burns, McAuley, Doidge (Harris 67), Driver (Daley 80), Bradbrook, Noble, Sweeney (Hayes 46), Collier, Mitchel-King, Crawford. Unused substitutes: Cornhill, Ibrahim.
FC Halifax Town: Glennon, K Roberts, M Roberts, Williams, McManus, Smith (Hatfield 56), Schofield, Marshall (Jackson 67), Pearson, Boden (Killock 86), Peniket. Unused substitutes: Senior, Hillhouse.
Referee: B Huxtable (Devon).
Man of the match: Danny Schofield.