Rather than a repeated global match you could capture what's inside the second set of parentheses and then use split, map and join to modify it in one go. (Note that I use the hex value for a single quote because I am running this as a one-liner in a *nix shell; you wouldn't need to do that inside a script.)

$ perl -E '
> $_ = q{(1,2,3) xxx (1,2,3)};
> s{([^(]+)(?=\)$)}{ join q{,}, map qq{\x27$_\x27}, split m{,}, $1 }e;
> say;'
(1,2,3) xxx ('1','2','3')
$
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I hope this is of interest.