How to replace two different characters with one character using preg_replace() function?

There is no need to use preg_replace.

Use str_replace instead:

$output = str_replace(array('@', '.'), '-', $input);

Since your search patterns are just strings, using string replacement using str_replace is better as suggested in other answer.

Here goes the preg_replace based answer:

$str = preg_replace('/@|\./','-',$str);