Swan and Thomas missed the Magpies' 88-point win over Melbourne on the Queen's Birthday - the former after he was sent to Arizona for a mid-season altitude camp and the latter with a one-week suspension - before last weekend's bye.
Malthouse said both players were better for the time off.
"He does [look rejuvenated], and so does Dale. Two weeks off … Dale's wasn't planned and Dane's has only came about at the end because he was very sore in a lot of areas so he will benefit from the non-contact and the repetition of [not] going into stoppages and being smashed," he said on Friday.
"His training hasn't backed off but the actual contesting hasn't been part of it for two weeks so I think both boys will benefit from it.
"It may not be easily seen in the first week but I think for a long term, you'll see a rejuvenated pair."
Malthouse said ruckman Darren Jolly, who also attended the US training camp, was always going to play in the VFL this week and would not have been considered even if Sydney Swans' big man Shane Mumford was not suspended.
He said he would need at least one game in the lower league to gain some touch before he returned to the side for the first time since Anzac Day.
"This wasn't a case of if Mumford was playing, Jolly would play; it was simply that we know after nine weeks, it's a long time out of football," he said.
"Given the first half of that he couldn't run and therefore was getting limited ball work … it's best he goes back and gets a bit of running touch, albeit on Sandringham's ground, which is about as big as your backyard, I guess."
The Pies' second bye came six weeks after their first in round seven, but Malthouse believes his players will get more from the most recent break after an intense few months that commenced with their successful NAB Cup campaign.
Despite the fact the majority of sides coming out of a bye have failed to win - including the Pies, who lost to Geelong in round eight after their first break - Malthouse said they hadn't done much different across last weekend.
"We didn't adjust it greatly but there's a few boys we sent home, the interstate fellas and a lot of the young country boys from around here went home, some wanted to stay here and had their parents and relatives come to Melbourne and spend the weekend with them," he said.
"My mind on that stuff is, the more you can disassociate yourself from football, because it's so constant for footballers, the better."
Malthouse was unable to explain why sides were having a tough time out of the bye, or why the Pies had beaten the Swans the past nine times they had played them.
"There hasn't been any easy wins whatsoever," he said.
"It's a great contest and you need to be switched on and ready for some very physical football because they are a good, strong football side who are at you all the time.
"They've got a certain amount of unpredictability but you basically know what you're going to get, and that is a great contest.
"Why have we won? We've won with different sides so it's no use saying the players are any better or any worse. There will be 11 players different from the last time we played them, collectively.
"There's no consistency in the players you put out there; maybe it's a bit of luck."
He also said he was confident defender Harry O'Brien would face the Swans despite a report emerging on Friday he suffered a compound finger fracture at training during the week, and then a bad reaction to antibiotics afterwards.
"As far as I'm aware he's playing," he said.
"He'll be fine, I'm sure."
