The regular '$' works just fine for me (Perl 5.8.8 on Linux, TT-2.20 — just in case it matters):

#!/usr/bin/perl

use Template;

my $template = Template->new();

my $input = q{[% "Blah, Blah," | replace(',$', '') %]};

$template->process(\$input) || die $template->error();   # output "Bla
+h, Blah"
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