Untested:

my $str = do {my $i; join "", map {$_ eq '(' ? $i++ : $_ eq ')' && $i 
+? $i-- : $_ eq ',' && $i ? ($_ = ';') : 0; $_} split '[(,)]', $str};
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This assumes the parenthesis are balanced.

But what should happen on:

    "(foo),(bar)"
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? The comma here is preceded and followed by a bracket - preceded by an opening paren, and followed by a closing paren even. If such a comma should be replaced as well, one might use something like (untested):

substr($str, index($str, "("), rindex($str, ")") - length($str)) =~ s/
+,/;/g;
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