I'd try this:

#!/usr/bin/perl -w
use strict;

my $test = "Bla bla bla;bla bla(foo; bar);bla blaBla bla bla; bla bla 
+(foo; bar); bla bla ";

$test =~ s/(\([^;]*);([^;]*\))/$1,$2/g;
print $test;
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That will replace all instances.