$text = "<tag#1>BLA</tag#2><tag#2>BLA</tag#2><tag#3>BLA</tag#3>";

$number = 1;

while ($text =~ s/<(.+?)#\d>(.+?)<\/(.+?)#\d>/<$1#$number>$2<\/$3#$number>/) {
$number++;
last;
}

print "$text\n";