Yes, the way you worded it sounds like you meant they both use the 95S with paintjobs on them.
What you wanted to say is that they both use racquets that have the PS 95S paintjob on them. When you say - "Both of them use a paintjob of the 95S...", that means they use a 95S with paintjobs on them.
I just wanted to chime in to say that the original phrasing was grammatically correct to begin with (with respect to what the original poster intended to say). The preposition "of" is used to describe the object following the preposition. In other words, "95S" describes "paintjob."
Other examples using the preposition "of":
1. That is a painting of a tree.
2. I graduated in the spring of 2004.
3. Everyday I drink three cups of coffee.
So back to the original sentence containing the prepositional phrase in question.
"Both of them use a paintjob of the 95S."
The sentence can have the prepositional phrase removed and make the same statement, albeit with less information.
"Both of them use a paintjob."
We can then ask ourselves, "What was the paintjob of?"
"It was a paintjob of the 95S."
We can apply this to any of the previous examples I listed as well.
"That is a painting."
"What is it a painting of?"
"It is a painting of a tree."
"Everyday I drink three cups."
"What do you drink three cups of?"
"I drink three cups of coffee."
"They both use racquets that have the PS 95S paintjob on them" is also correct, but I just wanted to say that the original sentence was correct as well.
If he had said, "Both of them use a paintjob
on the 95S," then there would be confusion.