Australia were on the brink of going 2-0 up but Stokes’ stunning unbeaten 135 powered England to an unlikely victory in the third Test at Headingley.
Smith, however, had to sit out with concussion after being struck by a 92 mph bumper from Jofra Archer at Lord’s.
The 30-year-old, who has been in imperious form on his Test return, is now set to play in fourth Test provided he comes through the practice match unharmed.
"Without Steve Smith playing I don't think we were given any chance of winning that Test match, I think most people wrote us off in that Test, so we're tracking ok," Paine told reporters after day one of the practice match against Derbyshire.
Marcus Harris was unbeaten on 52 while stand-in skipper Usman Khawaja was 18* as Australia were 77-0 in reply to Derbyshire’s 172.
Both Harris and Khawaja haven’t been at their best so far and one of them could make way for Smith.
"Steve Smith is going to come back in and play. So obviously someone from the last Test is going to miss out," said Paine, who replaced Smith as Australia captain.
"There's no doubt about that. You have the best player in the world coming back into your line-up."
England will be hoping to have James Anderson back in the side following a calf injury which saw him bowl only four overs in the first Test at Edgbaston.
Meanwhile, Paine insisted Australia had "moved on" from the Headingley Test.
"We had some honest conversations and we now we made some errors as a team and as individuals, but we can't be holding onto that," he said.
"We've moved on, we're ready for Manchester, the group's in a really good spot," added Paine, looking to lead Australia to their first Ashes series win in England for 18 years.
Stokes was dropped later in the innings by Marcus Harris.
Also Read: Ben Stokes’ Headingley miracle
The Durham all-rounder had another reprieve when he might have been out leg-before to Nathan Lyon.
But umpire Joel Wilson gave his ruling in England's favour although replays suggested Stokes would have been leg-before but Australia were unable to challenge the decision as they had no reviews left.
Lyon then later on missed out on a chance to run out Jack Leach at the non-striker’s end.
Paine, when asked on how Australia could get the better of Ben Stokes, replied: "Hold our chances would be a good start.
"I think Nathan Lyon in the last two Tests alone would have got him out five or six times had we held our catches or referred our lbws."
"Lyono's still a huge weapon against him," added Paine, rested from the Derbyshire match.
"But he (Stokes) is a world-class player, he puts bowlers under pressure and makes them do things and captains do things that you wouldn't normally do.
"That's a huge weapon England have got and one we've got to try and contain in the last two Test matches."