Lonergan, who has a very good record against star Swans recruit Lance Franklin, suffered a knock to the head midway through the first quarter in a clash with Leigh Adams.
He kept playing until quarter-time, but was given the red vest after being tested by the Cats' medical staff during the break.
Scott said the club chose to "err on the side of caution" in subbing Lonergan out of the game, with the Cats facing a six-day break between games for the second round in succession.
"I think he's a better chance (to play against the Swans) rather than not," Scott added.
"We hope (he'll be right), I guess. They've got a few big blokes down there."
When it came to the 20-point victory over the Roos, Scott was happy with the way his men snapped out of their recent form slump, which included losses to Port Adelaide and Fremantle and a narrow win over lowly Richmond.
He was particularly pleased that Geelong had 81 contested possessions to North's 61 in the first half.
"If you went back to post-game last week, we got absolutely smashed by a really mature Fremantle team around the ball and in the clearances, so we needed to fix that," Scott said.
"Those numbers were self-evident. I think we were minus-42 contest possessions (against the Dockers), and you can't win games of footy when you play that way.
"Early in the game, we used the ball quite nicely and were able to keep the ball off North Melbourne, but it started by winning it first."
The Cats were 41 points up early in the last quarter, then faded late and won by 20, but Scott wasn't about to blame the quick turnaround from last week's loss to the Dockers.
Questioned about whether his team ran out of legs in the closing stages, he said: "The scoreboard maybe suggests that a little bit, but I find it hard to judge.
"My instinct tell me probably not, but I'm not going to argue with anyone that says that's the case."
With suspended star Steve Johnson watching on from the stands, Geelong pushed fellow three-time premiership players Jimmy Bartel and James Kelly back into the midfield.
Bartel had spent a large part of previous matches in the forward line, while Kelly had been in the backline.
The duo prospered in the middle, with Kelly finishing with 33 disposals and Bartel turning in a best-on-ground effort that featured 32 touches and two goals.
"He's got a fair bit of footy left in him," Scott said of Bartel.
"He's had a terrific start to the year in a new role for him, and even tonight when we needed him around the ball, he was fantastic."
Tom Hawkins was another star for the Cats, hauling in seven marks and kicking 4.3.
"I thought he was really good," Scott said. "I struggle to compare it to other games, but he looked really dominant at times.
"I think his worth to the team was more than those four goals. He probably could've kicked a few more, but he was very strong in the contest."
Having consolidated its position near the top of the ladder, Geelong will now turn its attention to the clash with the Swans.
"It’s a game against a top-four contender on their home turf, so it will be a big game," Scott said.
"We're very confident that we'll be able to play near our best, which will be required."
