Step one is that you replace text between '@' delimiters. You can do that using

s/\@(.*?)\@/ ... /g;
[download]

Step two is to replace individual characters on the selected part.

Using the /e modifier you can use perl code in the substitution part, where you can use $1 as a normal variable. With a pair of "{}" delimiters on the right hand side, it can even look like normal code, as it looks like a block; you have to use similar paired delimiters on the left to make it work, for example using angle brackets "<>":

s<\@(.*?)\@>{ ... }ge;
[download]

So you might try to do the replacement using code directly in the substitution part. But, to be safe, you'd better call a sub to do the actual replacement, on the selected text. I'd change your code like this:

while(<>) {
    s/\@(.*?)\@/ subst($1) /ge;
    print;
}
sub subst {
    my $s = shift;
    my %r = (
        'a' => chr(0x430),
        'b' => chr(0x431),
        'c' => chr(0x446),
        'd' => chr(0x434),
        'e' => chr(0x435),
        'A' => chr(0x410),
        'B' => chr(0x411),
        'C' => chr(0x426)
    );
    $s =~ s/([a-eA-C])/$r{$1}/g;
    return $s;
}
[download]

Caveat: untested.

update: Tested, and bug fixed, this line was wrong:

    s/\@(.*)\@/ subst($1) /ge;
[download]

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