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Ramsgate must go through the play-offs after Cray Valley clinched the Isthmian South East title on the final day.
Rams lost at home to Three Bridges but their result was irrelevant as rivals Cray won 2-0 at Horndean to finish six points clear.
Ben Smith’s side trailed to goals from Ibrahim Jalloh and Noel Leighton before Joe Taylor replied from the penalty spot.
They’ll host Chichester - a side they beat 4-2 away a week ago - in the semi-finals on Tuesday night.
Sittingbourne meet Three Bridges in the other semi.
The Millers were already winning at Horndean - well on course for the point they needed - by the time Ramsgate fell behind.
And Rams soon conceded again with Three Bridges good value for their two-goal cushion at the break.
Ramsgate were out-of-sorts - perhaps resigned to their fate - and a busy Three Bridges side made them pay.
Things might have worked out differently - in terms of the result, if not the title - had anyone got on the end of Alfie Paxman’s dangerous low cross in the opening minutes.
Or had Benny Bioletti kept his shot down after rushing in at the back post to meet Joe Turner’s cross.
But Three Bridges had already threatened themselves through Jalloh, whose untracked run worked Tom Hadler, while Nabeel Ghannam wasted a good chance from Leighton’s pass.
Matty Warren made a fine challenge on Leighton before the visitors opened the scoring in the 26th minute.
Ex-Margate striker Leighton dropped deep to pick up possession and feed Ghannam whose right-wing cross was turned in by Jalloh.
Jalloh was denied by Hadler after a jinking run soon after but, from the resulting corner, the visitors grabbed their second with Leighton on target on the half-hour.
TJ Jadama fired over from distance for Ramsgate while Three Bridges had a penalty claim, for handball against Craig Stone, turned down just before the break.
Ghannam, with the goal at his mercy, wasted a golden chance to add a third after the impressive Jalloh led a rapid counter-attack at the start of the second half.
He still won’t know how he didn’t score.
Rams were back in business in the 58th minute when Medy Elito was brought down in the box by Bryan Villavicencio, after TJ Jadama won and played a quick corner to Lee Martin.
Taylor stepped up and fired home down the middle for his 53rd goal of the season before making way for Jack S Paxman, making his comeback from a metatarsal injury.
Leighton went on to hit the post after Warren lost the ball in midfield, as Bridges went close to restoring the two-goal lead.
And the visitors had another strong penalty claim after Alex Brefo wrestled Jalloh to the ground before Hadler did well to thwart Leighton from close range.
Ramsgate pushed hard for an equaliser but were out of luck, ending the season with 89 points.
Ramsgate: Hadler, Stone, Warren, Brefo, Bioletti, Martin (Parter 69mins, Elito, Jadama (JA Paxman 69mins), A Paxman, Taylor (JS Paxman 61mins), Turner. Subs not used: Green, Christie.
Three Bridges: Sheik, Ferriera, Woolard, Villavicencio, Jalloh (Hanslow 83mins), O’Neill, Leighton, Ghannam (Adam 73mins), Euba, Irving, Difika (Donaghey 86mins). Subs not used: Anderson, Bendall.
Referee: Deryll David.
Attendance: 1,464.