Yes you can place the Pyrex lid on the hot dish and it will be just fine.
The Pyrex dish lid is made to withstand the temperatures of the hot food so it will not harm the Pyrex lid if you put it on the food dish when hot.
I've used the Pyrex lid on hot dishes before and never had a problem doing so.
If you plan to put the Pyrex dish into a carrying case then you should put the Pyrex lid on the hot dish within a few minutes of removing it from the oven and place it into the carrying case to keep the food at a hot enough temperature to avoid bacteria growth on the food.
If you're gonna put the hot food into the refrigerator then that is fine as well and it will cool it down but I would wait a few minutes to allow the Pyrex dish to cool down at least somewhat.