Lyon also declared that Freo was still "well and truly alive" this season at 6-7 and 12th on the ladder.
Although reluctant to look ahead to Freo's next month that sees it play Western Bulldogs (14th), Melbourne (16th), Greater Western Sydney (17th) and Port Adelaide (15th), Lyon remains optimistic and expects to regain playmaker Stephen Hill next round and possibly defender Zac Dawson.
Lyon principally put Freo's loss down to its overuse of handball early in the game - it had 64 handballs and just 50 kicks in the first quarter - and its inability to combat Collingwood's elite midfield at centre bounces.
But he was buoyed by Freo's effort to cut a 40-point point deficit early in the second quarter to just 17 points at the 21-minute mark of the third term.
"I know this effort is going to stand us in really good stead going forward [and show] that we're a team that, no matter what result we were getting, we just kept persisting and persevering against what is a really good team," Lyon said.
"So we take a bit out of it ... we walk away thinking, 'yeah we've lost but at a deeper level there was a bit to like about our persistence and perseverance'.
"I'm really confident we're a team that turns up and gives effort almost regardless. So it's a nice feeling as a coach but we can't be complacent with that."
Lyon said Fremantle's fightback had come after he'd instructed his players to go one on one with their Collingwood opponents all over the ground.
But it was Freo's chase-down tackles when Collingwood players seemed headed for easy goals and the leadership of his senior players such as skipper Matthew Pavlich that pleased him most.
Lyon said Fremantle's poor start to the game, which saw it go goalless until the 17-minute mark of the second quarter, had nothing to do with his team not being switched on.
"We certainly came to play. We won the ball really well early ... in the first five or six minutes," Lyon said.
"We have some really opportunities inside forward 50 to go forward that we didn't do very well with [and] they took it down the other end.
"We mucked around with the ball a fair bit. I thought we handballed way too much but that was a credit to their pressure."
Lyon said his team's ball use and centre bounce work had to improve but stressed such things were easier to fix than a lack of effort.
"We can fix the mechanics and keep adding talent to the group as long as we keep growing with that sort of effort," Lyon said.
"Are we the perfect list and group at the minute? No, but we're certainly building.
"When you look at the list management models there's [opposition] midfield groups with six or eight [players] with 150 games ... so (Matt) De Boer, (Nick) Lower, (Tendai) Mzungu, (Clancee) Pearce they're 21-22 year-olds with 30-40 games...
"(Nathan) Fyfe, (Stephen) Hill and (Anthony) Morabito will return. And we'll attract talent to the club and you'll blink and say 'How did all that happen?'
"So we've got a strong plan but it only comes to fruition when you continue to compete like we did today."
Nick Bowen is a reporter for AFL Media. Follow him on Twitter: @AFL_Nick
