The Blues conceded six unanswered goals in the final term of their 38-point loss at Etihad Stadium, but Malthouse wasn't concerned one month out from the club's season opener against Port Adelaide.
He said the successful returns of Thomas, Kade Simpson, Heath Scotland, Michael Jamison, Jeff Garlett and Matthew Kreuzer were more important than running out matches in February.
"I said to the players before the game, 'If we win we'll tick it, if we lose I'll make an excuse for the media' … but I don't have to make an excuse," Malthouse said.
"It was almost predictable that six of our players that had been out of action, coming back, were never going to impact the last half.
"It was most important that they actually got running-around minutes. In this case most of them played approximately the minutes we wanted them to play."
Malthouse was happy with Thomas's first match under his direction since the pair was at Collingwood in 2011 and said he "gave us a bit", finishing with 18 possessions but winning just two in the final term.
He said the NAB Challenge had been a success for the Blues, who beat North Melbourne by seven points in their opening match and now face the Western Bulldogs in a practice match.
"We couldn't possibly get three better sides leading into our season to test certain areas of our game," he said.
"I thought we were better this week than we were last week, and we expect to be better next week in some of our mechanisms."
On reports linking midfielder Bryce Gibbs to Port Adelaide at the end of the season, Malthouse said: "I have a very good feel (on Gibbs). I've got a good feel."
He said free agency was bound to be two-tiered in the AFL, disadvantaging smaller clubs.
"You won't get too many bottom sides attracting free-agent players who will make a massive difference," he said.
"But you will always get the top sides who are going to be able to attract free agents from the bottom sides."
Twitter: @AFL_Nathan
