When you’re outputting the field in your template, use PHP’s number_format.
Example:
<?php echo number_format( floatval( get_field('price') ), 2, '.', ',' ); ?>
floatval
converts the custom field string into a float, and number_format
constrains the number to 2 decimal places, and adds the comma.
On the admin side there doesn’t seem to be an easy way to add a comma to the “Number” field type.