Macaffer, a late inclusion for the ill Leon Davis, was subbed in for a tired Andrew Krakouer at the 16-minute mark of the final quarter.
"There was a thought process that I wasn't going to make that change at all and leave him there and go with three because then it forces the other boys to get that little bit more into them, and you come out the other side [more tired] but probably in the long run fitter," Malthouse said after the win at Etihad Stadium.
"Now, we had a couple of boys with cramp so it was a good opportunity.
"I certainly did toy with not having a 22nd player play to lift up the game time for everyone."
Malthouse's plan for his players over the next six rounds until the Magpies' first bye in round seven was to ensure about 30 of his players, as in 2010, enjoyed a reasonably even level of game time.
He said that meant the weekend's work wasn't over yet for Macaffer, who had a Sunday morning training session booked in.
"He'll train and he'll train hard. Will he simulate match practice? No he can't," he said.
"We just need to get some work into him and he will be seriously considered for next week.
"These are the dilemmas we will all be confronted with. How much game time does your sub get, and more importantly, how much game time does he get over a period of seven or eight weeks?"
The Magpies also have Nick Maxwell, Tyson Goldsack, Cameron Wood and John McCarthy to come into consideration over the next few weeks, while Malthouse said Lachlan Keefe, Alex Fasolo, Ben Sinclair would be in line to make their debuts.
He said Macaffer's explosive inclusion into Saturday's game was an illustration of how tough the step up between the pre-season competition and season proper was.
"He came on fresh and you could just see … what he was able to do - all the other players looked like they'd just jumped on a slow bus and he was down here at Albert Park," he said.
"That gives you an illustration of the tiredness of the players by the end of the game.
Malthouse was pleased with the even performance against Port and attributed the Pies' third-quarter lapse, which saw the Power move within 16 points, to falling away at the stoppages.
"The end result looks good, but there were a few ups and downs," he said.
"I think anyone who underestimates Port are going to be in for a nasty shock."
