Following yet another tumultuous week as a resolution to the supplements saga draws near, the Bombers put their off-field woes aside to turn a 20-point third quarter deficit into a 12.10 (82) to 9.22 (76) victory in front of 53,630 fans.
That Zaharakis kicked the winning goal was fitting, given it was he who sparked the late fightback with a superb 11-disposal final quarter.
The win snapped a dismal four-game losing streak for James Hird's men, which had seen them tumble from second to seventh on the ladder.
"It was a terrific win," Hird said.
"It just shows the courage and the heart of the players we've got.
"I think to come out and play that way after the week we've had is pretty amazing."
But the inspiring effort may be in vain, with negotiations between the club and the AFL appearing increasingly likely to see Essendon stripped of premiership points and removed from this year's finals.
Reports have also suggested that Hird could receive a lengthy suspension as part of the negotiated outcome, something he said he may be prepared to accept if it spared the club harsh penalties.
The loss ends Carlton's hopes of overtaking Port Adelaide in eighth, but with ninth place now a chance to be enough for a September berth, the Blues remain in finals calculations.
However, a furious Carlton coach Mick Malthouse said he did not wish to consider that possibility.
"Not one little bit interested," he said.
"We came here tonight to win, and we didn't win.
"I don't know what's going to take place, I don't care what's going to take place.
"We play Port next week, and technically we can't make the eight."
Bombers skipper Jobe Watson, booed by Carlton fans every time he went near the ball, led his team with distinction, gathering 27 disposals and booting two goals in the face of a close tag from Bryce Gibbs.
Brendon Goddard also had 27 touches, while fellow midfielder Heath Hocking went head-to-head with Marc Murphy, with both players finishing with 22 disposals.
Hocking is certain to face scrutiny from the Match Review Panel for an elbow to Chris Yarran's head during the third quarter.
Michael Hurley kicked three goals and hit every contest with aggression, while Stewart Crameri contributed two despite struggling with a sore right ankle.
For the Blues, veteran midfielder Kade Simpson was a standout, gathering 32 disposals.
He almost single-handedly saved the game in its final moments, twice putting his body on the line to take a mark and then win a free kick on the last line of defence.
Small forward Yarran played one of his better games for the season, booting two goals and chasing, tackling and blocking with intent.
Tom Bell and Mitch Robinson were other useful contributors, but Malthouse's team was ultimately left to rue their dismal 29 per cent conversion rate in front of goal.
The Blues were dealt a double blow 90 minutes before the bounce, with key players Andrew Walker (gastro) and Matthew Kreuzer (calf) both late withdrawals.
They then lost Brock McLean during the first quarter with a right quad injury.
Walker and Kreuzer's absence opened the door for forgotten backman Nick Duigan to play his first senior game since round one, and the South Australian responded with 13 disposals and 0.2.
Despite Malthouse's protestations otherwise, both clubs' attention will now turn to Monday's meeting between Essendon and the AFL Commission, at which a resolution to the Bombers' charge of bringing the game into disrepute is expected to be reached.
CARLTON 3.9 5.10 9.18 12.10 (82)
ESSENDON 4.2 6.7 8.7 9.22 (76)
GOALS
Carlton: Menzel 2, Yarran 2, Tuohy, Henderson, Gibbs, Betts, Armfield
Essendon: Hurley 3, Watson 2, Crameri 2, Zaharakis, Ryder, Myers, Kommer, Goddard
BEST
Carlton: Simpson, Yarran, Scotland, Bell, Curnow, Robinson
Essendon: Watson, Hurley, Hocking, Goddard, Pears, Myers
INJURIES
Carlton: Matthew Kreuzer (calf), Andrew Walker (gastro) replaced in selected side by Nick Duigan and Aaron Joseph, Brock McLean (quad)
Essendon: Crameri (ankle)
SUBSTITUTES
Carlton: Nick Graham replaced Brock McLean (quad) in the first quarter
Essendon: Ben Howlett replaced Alwyn Davey in the third quarter
Reports: Nil
Umpires: Stevic, Stewart, Mollison
Official crowd: 53,630 at the MCG
