Thomas, who has played all nine games for his new club this season after battling ankle issues, gathered 22 possessions (including a season-high 16 kicks) and laid five tackles at the MCG to be a solid contributor in another momentum-building victory for the Blues.
Most pleasing for the Blues army, including his coaches, was Thomas' effort to nail a set shot from 45 metres midway through a tense final term, having previously struggled with distance and accuracy.
He still appears to be lacking his renowned line-breaking speed, but Malthouse expects he will gradually improve with match fitness.
"It’s a reconstruction – it takes 12 months (and) he’s six weeks in front of what everyone thought," Malthouse said post-match.
"We didn’t expect him to play the first six games because we were building him up to play, and it will take him time … He is going to step up."
Of Thomas' crucial conversion, Malthouse said: "We were all very happy for his goal, put it that way. It's good for him because it's not through a lack of effort."
Malthouse lauded the tagging jobs performed by Andrejs Everitt and Dennis Armfield on Rory Sloane and Patrick Dangerfield respectively, and also lauded best-afield vice-captain Kade Simpson for his courage after copping a heavy knock early.
"He's (an) extremely brave player," Malthouse said.
"We tend to say, 'Who's the bravest player?' and it's generally someone who's big and tough and knocks 'em over … He is in the same class as two or three others that just, at that weight level, don't know how to back off.
"His bravery is outstanding, and it comes on the back of a broken jaw a couple of years ago … and probably being 75-76 kilos, and leadership through action."
Malthouse was satisfied with the desperation shown by his team overall, which he said proved decisive late in the seesawing clash.
"Overall to defensively just hold out and still have control … of the occasion – that is so vital," he said.
"Perhaps this time last year we may have made the mistake of being a bit extravagant or being less mindful where the boundary was or having less support perhaps around you. Just little things like that.
"There was some good blocks, a good punch back, there was a good contest … Some of those things during the last five minutes (were) pretty hectic."