my $str      = 'Fsih my test variable is fsihd or is it gfsih or gfsih
+d fsih';
#                                        1111            2222     3333
+  4444
my $substr   = 'fsih';
my $regexp   = qr/\Q$substr\E/;
my $replace  = 'fish';
my $instance = 3;  # 3rd

print("$str\n");

my $pre_count = $instance - 1;
$str =~ s/((?:$regexp.*?){$pre_count})$regexp/$1$replace/;

print("$str\n");
[download]

You might have noticed both of these are case sensitive. Both can be made case-insensitive. The non-regexp version is most likely much faster. The regexp version can handle regexps instead of constant strings.