use Data::Dump;

my $data = q|
foo
bar
{{
alpha
beta
}}
baz
|;

@splits = split /({{.*?}})/s, $data;

dd \@splits;

my $result="";
while (my $block = shift @splits) {
  $block  =~ s/\n/<br>\n/gs;
  $result .= $block;
  $result .= shift @splits if @splits;
}

print $result;

##</code><code>##

["\nfoo\nbar\n", "{{\nalpha\nbeta\n}}", "\nbaz\n"]
<br>
foo<br>
bar<br>
{{
alpha
beta
}}<br>
baz<br>