I think that to make it work the way you tried, you need to have the call to diff return a list context. Try this,

@lines = (`diff $args $file1 $file2`);
for (@lines) {
  print;
}
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It may not be exactly what you want, in that it captures all of the output into an array.

Or, if you really want the output from diff in a scalar as a single string, then you need to (temporarily) change the input record separator $/ to something other than newline, typically the null value will suffice. This snippet will accomplish the task:

{
  local  $/ = '\0';
  $line = `diff $args $file1 $file2`;
  print $line;
}
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bedk's solution is probably better because you can filter the output from diff one line at a time through a regex, and save/process only the lines you want.
Cheers,
PCS