The Marina Bay track wasn't expected to suit Williams but Albon had a solid race, and a stop for new tyres under the Virtual Safety Car, mirroring the strategy used by Mercedes, gave him extra pace in the latter stages of the race.
Albon was in 10th and closing on Liam Lawson when Perez made contact as he tried to overtake in a late-race incident that wasn't shown on TV.
The Red Bull driver subsequently received a five-second penalty and a penalty point on his licence.
Albon recovered to finish 11th, but Vowles says that he would have passed Lawson and then moved up to eighth when George Russell crashed on the final lap.
Thus the Perez incident in effect cost Williams four points, while gifting one to AlphaTauri through Lawson, and one to Haas via 10th-place finisher Kevin Magnussen.
With seven races to go, Williams lies seventh in the world championship on 21 points, ahead of Haas on 12, Alfa Romeo on 10, and AlphaTauri on five, with each place difference representing millions in prize money.
"Quite a few points on the table were taken away," Vowles told Motorsport.com.
"It is frustrating that when you're in a championship that's being fought down to the point, and you're leading against your direct rivals in this championship, to have it taken away from you hurts.
"And without good reason either. It was a lunge – there are sensible ways of overtaking and that wasn't the way to do it.
"For a number of laps prior Perez was very much on the inside and trying to put his nose there. That in itself isn't a problem, you've got to do aggressive techniques.
"But Alex had already committed to the turn-in point. And it's overlapping at the back and it was contact into the sidepod. There was no way that was going to work.
"So it's incredibly frustrating. You are into fine, fine margins. And this could be what decides the championship positions."
On the plus side, Vowles said that the race showed once again that the team is in good form and making the right calls.
"The main thing is I think you can see the team really giving it their all, and Alex giving his all," he said.
"We know we were on the backfoot this weekend, but we made a set of really good decisions that actually didn't necessarily all happen in the race – the decision to have two mediums took place weeks ago.
"But that all came to fruition when that VSC came out. And the ability to take those opportunities is great. And it was fantastic to see Alex fight through again."
Vowles was encouraged by the fact that traditionally the Singapore track has not favoured the team, which suggests that the car could be good at other races in the last part of the season, with sprint weekends and the threat of rain at several venues adding to the mix.
"If you look back at the history of this team, we haven't had cars in Q2 in Singapore since 2016," he noted. "So actually, the problems are more fundamental in what we're doing as a base.
"I think we will be competitive again, although perhaps not Zandvoort level. There is opportunity, but in both directions, lots of opportunity for others to get a very good score, or us to walk away with more points.
"What I believe it is if you look at the progress we've made as a team, we're now going to most races with Williams as a car that can score points."
