Fremantle will not appeal the decision after Fyfe's attempt to get the charge downgraded from intentional to reckless was unsuccessful. He will now miss matches against Gold Coast and Collingwood.
"Yeah, (we are) really disappointed," Fremantle coach Lyon said on Wednesday.
"Nathan wasn't thrilled with the intentional grading, and thought there was an opportunity (to fight the charge)."
Fyfe could have accepted the Match Review Panel's findings and only missed one game, which in hindsight, according to Lyon, might have been a better decision.
"Maybe we should have priced the risk greater, because it really hurts now," he said.
"But we live and we learn.
"At the end of the day we respect the umpire's decision."
Lyon believes the Suns present a really dangerous challenge for his side in the absence of Fyfe, Aaron Sandilands, Matthew Pavlich and Kepler Bradley.
"We acknowledge Gold Coast have really developed and improved," he said.
"Last year, we went up there without a deep understanding of them and, really, almost got beaten.
"They’ll have belief they can beat us, it’s their home turf, they’ve really grown.
"For us, it’s a red alert and we’ve got to handle the travel well – which we do – but we’ve got a lot of improvement in us.
"With Nathan Fyfe out, we need to step up."
Freo defender Alex Silvagni is in line for a shock recall as a forward as the Dockers attempt to patch up their injury-hit attack.
With Pavlich, Bradley and Sandilands all sidelined, and Zac Clarke needing a run in the WAFL after a recent calf injury, Fremantle is light on for tall options in attack.
One-game defender Tanner Smith is a strong chance to be thrust up forward in Saturday night's clash against Gold Coast at Metricon Stadium, while Silvagni is also in the mix after overcoming a recent ankle injury.
Silvagni has played the majority of his 29-game career as a key defender, but was trialled up forward with limited success during the pre-season.
Lyon is yet to decide how to structure his forward set-up against the Suns, but said Silvagni and Smith were two viable options.
"He's a powerful man. A great competitor. And he's played those roles before," Lyon said of Silvagni, who played only five games last year.
"We'll weigh up where he's at.
"We'll never doubt his commitment to the team and the effort and his hardness. He's such a powerful man. He'll be a handful. He's certainly in calculations."