#!/usr/bin/perl

my $template_line = "bla bla bla [VAR01] bla bla [VAR02] bla [VAR999] [VAR99] bla blubb";
my @Vars = (0..99);

$template_line =~ s/\[VAR(0[1-9]|[0-9]{2})\]/$Vars[$1-1]/eg;
print $template_line;

bla bla bla 0 bla bla 1 bla [VAR999] 98 bla blubb