The Bombers led by five points midway through the second quarter, but surrendered meekly in the heat as Fremantle slammed through 10 unanswered goals to set up the 18.5 (113) to 9.6 (60) victory.
WATCH: Suban strikes
Bombers veterans Dustin Fletcher (soreness) and Paul Chapman (ankle) didn't make the trip west, while Essendon was dealt another blow when David Myers became a late withdrawal.
And the bad news kept coming for the Bombers, who were forced to sub Goddard off early in the second quarter.
Goddard received treatment on his groin before the match, and he was clearly troubled as he hobbled through the opening term before Essendon pulled the plug on his day. The Bombers could not have replaced him after flying with 23 players.
"I didn't know about (Goddard) until the first quarter," Thompson said.
"We didn't know David was going to pull out ... it was literally only five minutes before we got on the bus that I found out he wasn't playing. So that's rare. If you leave two out, then they don't get to play."
Fremantle was also dealt a blow when star midfielder David Mundy was subbed out in the third quarter due to concussion.
The Bombers matched Fremantle for most of the opening half, but were blown off the park in the third quarter as the 30-degree conditions took their toll.
Fremantle booted the last three goals of the first half to take a 13-point lead into the long break.
WATCH: Danyle Pearce's over the shoulder snap
But it was the Dockers’ third-quarter blitz that tore the heart out of Essendon, as Fremantle ran rampant kicking seven straight goals.
"We are certainly not getting carried away with it, both teams had some personnel challenges," Ross Lyon said.
"It was always going to be in extreme conditions and coming from the eastern states that is always going to be difficult.
"When you look at their outs, the three they lost (in) Fletcher, Chapman and Myers, we are under no illusions that we didn’t quite play the Essendon that we expected to be playing."
Skipper Matthew Pavlich (three goals), ruckman Aaron Sandilands (45 hit0-outs), and defenders Luke McPharlin and Michael Johnson were crucial in the win.
Speedsters Stephen Hill, Danyle Pearce and Hayden Ballantyne added vital class in the absence of Nat Fyfe, Michael Barlow, Michael Walters and Chris Mayne.
Bombers trio Dyson Heppell, Brent Stanton and Michael Hibberd tried hard for the Bombers.
However, the absence of key talls Paddy Ryder and Tom Bellchambers proved telling as Fremantle ruckman Sandilands enjoyed a field day against Jake Carlisle and Joe Daniher.
Sandilands will hope his high whack on Travis Colyer in a clumsy tackle attempt will go unpunished by the Match Review Panel.
WATCH: Sandi and Hilly's chemistry
As the temperature hovered about 30 degrees for most of the match, Fremantle youngster Lachie Neale stuck his head in an esky in a bid to escape the heat.
The Bombers were also looking for a place to hide after an embarrassing third quarter, and the visitors managed just 30 inside-50s for the match.
FREMANTLE 2.1 6.3 13.4 18.5 (113)
ESSENDON 2.1 4.2 5.4 9.6 (60)
GOALS
Fremantle: Pavlich 3, D. Pearce 2, Taberner 2, Neale 2, Hill 2, Crowley, Mundy, Suban, Ballantyne, McPharlin, Mzungu, Clarke
Essendon: Hardingham 2, Watson, Daniher, Gleeson, Winderlich, Jetta, Stanton, Melksham
BEST
Fremantle: McPharlin, Johnson, de Boer, Hill, Pavlich, Sandilands
Essendon: Stanton, Heppell, Gleeson, Baguley, Hibberd
INJURIES
Fremantle: Mundy (concussion)
Essendon: Paul Chapman (ankle) replaced in selected side by Leroy Jetta, David Myers (illness) replaced in selected side by Travis Colyer, Dustin Fletcher (soreness) replaced in selected side by Dylan van Unen, Brendon Goddard (groin)
SUBSTITUTES
Fremantle: Josh Simpson replaced David Mundy in the third quarter
Essendon: Leroy Jetta replaced Brendon Goddard in the second quarter
Reports: Nil
Umpires: Margetts, Nicholls, Hosking
Official crowd: 36,722 at Patersons Stadium
