The Hornets enjoyed a dream start as Dan Ajakaiye fired the hosts in front after just 100 seconds.
Reece Myles-Meekums doubled Horsham’s advantage on 74 minutes, but the Stones set up a nail-biting finale when Ben Brookes slotted home from the penalty spot with two minutes to go.
However, the National League South outfit were unable to find a late equaliser, leaving the Hornets as the only Isthmian Premier side remaining in the competition.
The draw for the third round of the FA Trophy will take place today (November 18) at 3.15pm on talkSPORT 2.
Horsham are back in cup action tomorrow (November 19). The Hornets’ defence of the Sussex Senior Cup continues as they welcome Eastbourne Town to the Fusion Aviation Community Stadium (kick-off, 7.45pm).
See some of John Lines’ pictures from the game on this page and the ones linked, and read Horsham manager Dominic Di Paola’s thoughts in the West Sussex County Times, out every Thursday.
37. FA Trophy: Horsham FC upset division-above Maidstone to reach third round - the match in pictures
Action from Horsham v Maidstone Photo: John Lines
38. FA Trophy: Horsham FC upset division-above Maidstone to reach third round - the match in pictures
Action from Horsham v Maidstone Photo: John Lines
39. FA Trophy: Horsham FC upset division-above Maidstone to reach third round - the match in pictures
Action from Horsham v Maidstone Photo: John Lines
40. FA Trophy: Horsham FC upset division-above Maidstone to reach third round - the match in pictures
Action from Horsham v Maidstone Photo: John Lines