Quickly, I might not have caught everything

• 'g' modifier in an if is almost always wrong. It is wrong here.

• $2 in s/.../$2/ refers to the second capture in ..., not some earlier capture by some other match or substitution operator.

• The search expression appears to be text, not a regexe, but you use it as a regexp.

• Using $_ in $_ =~ s/$1/$2/g; and print $_; defies the purpose of using $_.

for my $line (@lines)
{
    for my $replace (@replaces)
    {
        my ($s,$r) = $replace =~ /\\replace\t(.+?)\t(.+?)\n/
            or next;

        $line =~ s/\Q$s\E/$r/g;
    }

    print $line;
}
[download]

Update: Actually, that's a bad approach since you have to keep recompiling regexps. Reverse the nesting of your loops:

for my $replace (@replaces)
{
    my ($s,$r) = $replace =~ /\\replace\t(.+?)\t(.+?)\n/
        or next;

    s/\Q$s\E/$r/g for @lines;
}

print @lines;
[download]

Update: Woops, I was still using $2. Switched to $r.