Thompson wouldn't use the Perth heat his team encountered in round four - or the six-day break that followed - as an excuse for the Bombers' 16-point loss at Etihad Stadium.
But after slipping to 2-3 ahead of the Anzac Day blockbuster, he said his players weren't physically or mentally ready to face the Saints, who outscored his team 10.9 to 4.11 in the last three quarters.
"As a club we didn't go in ready … it's a shame, we missed a great opportunity," Thompson said.
"I'm not sure how much recovery sessions our boys have done (after the Perth trip). I know that the good players I've had experience with over the years would have done twice as much.
"They would have reported and they would have got more massage and they would have eaten right and slept well and just done everything right so if it got to that point they could find something to get the team over the line."
Thompson praised the Saints, who were "fast, skilful, had good balance of corridor ball [and] knew when to slow it up".
Beaten in the clearances (34-30), contested ball (123-120) and tackle count (49-48), he said his team "just didn't handle any of it".
"Everyone probably thought we should have beaten St Kilda – I certainly did – but you need to be able to finish the job and just do it," he said.
"You don't have to play your best football, you don't have to feel in the greater shape. But you just find a way to win because that's what you need to do."
Tall forwards Jake Carlisle and Joe Daniher went goalless on Saturday night and gathered just nine possessions each, with the return of Patrick Ryder also failing to give the Dons a ruck advantage.
"They spent a lot of the night competing against numbers and that's something we don't like to allow," Thompson said of his forward targets.
"You can say they didn't play well, they didn't because we didn't kick enough goals, but it was a team thing, not just a forward thing."
A gastro bug has swept through the Bombers camp over the past two weeks, but Thompson said no new players had been struck down for four days.
He said half-forward Jason Winderlich would return for the Anzac Day clash against Collingwood while run-with specialist Heath Hocking would be clear to play after being substituted out with a hand injury on Saturday night.
"He got stomped on and he's got tight groins – it was just a combination," Thompson said.
"He's a very important player. He'll probably play on a (Dane) Swan or a (Scott) Pendlebury, whoever's down there for Collingwood on Friday.
"We just let him have some legs."
