Last week Mercedes announced the bombshell news that seven-time world champion Hamilton would be departing the team at the end of 2024 to join his former GP2 team boss Fred Vasseur at Ferrari.
According to Vowles, Hamilton's shock departure will inevitably be a blow to Mercedes, but he believes all parties will come out stronger.
"I actually think it's good for the sport," he said at the launch of Williams' 2024 livery. "It'll be good for Lewis, because he'll learn from it and he will challenge himself.
"It's not good for Mercedes short term, but actually, I think you're going to see they're going to be absolutely fine on where they get to on drivers.
"They have a strong lineup that they can pick from. They will come back stronger as a result. So, ultimately, it's a good thing all around in time."
While the timing of Hamilton's decision was unexpected, Vowles says he is not surprised that Hamilton was ready to step out of his comfort zone at Mercedes and change environments.
"I had a chat with him the weekend, it was a hard decision for him," he said when quizzed further by Autosport. "First and foremost, it's been his home and his family for many years.
"And it's the same as any of us when we're going to change organisations and move elsewhere.
"It causes you to tear inside, but he wants to prove to himself and prove to the world that he can go through one of the hardest things you ever do, which is transition to a new organisation, and still come out successful.
"He probably had one chance remaining in his career to prove that, and I completely understand the reasons why."
Williams driver Alex Albon said learning of Hamilton's headline move was a "pinch yourself moment", likening it to football icon Lionel Messi leaving his long-time home of FC Barcelona for PSG in 2021, then linking up with David Beckham's Inter Miami team in 2023.
"What a new story it was. I don't know about you guys but I definitely didn't see it coming," Albon said. "But good for him, I think he wants that change.
"The timing of it is obviously awkward more for it being the week before all the teams are doing their announcements.
"It just shows you how big Lewis is, seeing the stock of Ferrari going up as much as it did and just seeing the general perception of the news.
"Definitely to me, it was one of those pinch yourself moments, like 'Is this a real story?'
"There are so many rumours going over the winter, you didn't know what had any credibility or not. And the Ferrari one definitely seemed to be a rumour to me at the very beginning of the story, and then it turned out to be a real thing.
"It reminds of the Messi-Miami transfer and just shows you the appetite for Formula 1. It leaves a lot of questions in the driver market as well and opens that up."
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