The Blues came back from 27 points down in the third quarter against the finals-bound Bombers after coughing up a six-goal lead in the first half.
Malthouse said he felt his team worked hard enough to win and the inability to get the runner out to every player when Bryce Gibbs was lining up for goal with less than a minute left hurt them.
WATCH the dramatic final two minutes
Gibbs’ shot from 45-metres came up short and the Blues weren’t able to punch it through for the rushed behind which would have won the game.
Malthouse said he felt satisfied with how his players rallied and didn't allow the result to become a blow out.
"We had the last two or three shots and we just couldn't put it over the line," Malthouse said.
"We didn't get to every player unfortunately with the time; one player thought it was 27 minutes and wanted to keep it in play.
"If they had said 15 seconds left, I guarantee it would have been punched through.
"But I'm pleased we fought back when the game could have been absolutely taken from our grasp [with] no comeback whatsoever in the second quarter and early in the third quarter.
"I am buoyed by the players' resolve."
Malthouse said it was "too simplistic" to believe his players had nothing to fight for going into the game, given their position outside the top eight.
But he said playing five finalists in the past six weeks had given his players "a great education".
"It's taught us lessons we can add to. It's only half the result we're looking for but nonetheless it's a result that gave us something to move forward from," he said.
The Blues' start to the season was dismal, or "ordinary", as Malthouse called it, with five losses from the first eight rounds.
But he said players taking on leadership roles and developing from them was a positive to take from the second half of the season.
He also said he believed the team was more understanding of his approach and would enter 2015 better for that.
"I think the players have got the knack of what I want in terms of commitment and game plan," he said.
"We've had to juggle it and juggle it until we've found the best source to suit them to play their best football, and that takes some time because at every club there’s a variable.
"We’ll enter into our new pre-season with a buoyancy that says we know what we have to do, let's work to it."
