What you need is a way to capture the output from the java app without invoking an intermediate shell. Then your command line arguments will not get re-interpreted. A good standard module for this is IPC::Open3. Try something like this: 
use IPC::Open3;

sub backticks {
  my $pid = open3(my $wfh, my $rfh, 0, @_)
              or die "open3 failed: $!";
  close($wfh); # assume the script needs no input
  my $output;
  while (<$rfh>) { $output .= $_ }
  close($rfh);
  $output;
}

my $java_output = backticks('java', '--classpath=...', ...);

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In reply to Re: CLASSPATH problem when using backticks by pc88mxer
in thread CLASSPATH problem when using backticks by maithree

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