With the contest effectively a pool grand final after both sides accounted for the Lions earlier in the evening, the Bombers fell to a 22-point half-time deficit but dominated the second half.
Essendon had 14 inside 50s to the Saints' three after half-time, but were unable to convert until an Angus Monfries snap at the eight-minute mark, as St Kilda applied its renowned defensive pressure.
Goals to Jake Carlisle and impressive rookie Stewart Crameri brought the margin to three points, before the Saints steadied through Leigh Montagna. But the Bombers refused to lie down.
Brent Stanton received a 50-metre penalty at the 20-minute mark, narrowly missing his super goal attempt that would have put James Hird's side in front, before former Hawk Williams took a contested mark and calmly slotted his shot from outside 50 after the siren to tie the match.
Earlier, Essendon kicked the first goal of the game through an opportunistic snap from Crameri, but the Saints hit back immediately when former Cat Ryan Gamble marked and converted from 30 metres.
From there St Kilda started to gain control, with goals to 2010 draftees Tom Ledger and Will Johnson and two to Stephen Milne, putting the Saints 22-points clear at half-time.
Essendon will now take on Melbourne at Etihad Stadium next Thursday night.
St Kilda 0.5.2 0.6.2 (38)
Essendon 0.1.4 0.5.8 (38)
GOALS
St Kilda: Nine-point goals: Nil Goals: Milne 2, Gamble, Ledger, Johnson, Montagna
Essendon: Nine-point goals: Nil Goals: Crameri 2, Monfries, Carlisle, Williams
BEST
St Kilda: Gamble, Goddard, Armitage, Milne
Essendon: Dempsey, Crameri, Monfries, Stanton
INJURIES
St Kilda: Nil
Essendon: Nil
Reports: Nil
Umpires: Meredith, Mollison, Ryan
Crowd: 24,158 at Etihad Stadium
The views in this article are those of the author and not necessarily those of the clubs or the AFL.