Both of your expressions are good and natural. I would not say “The sky is clear”

Ali, either one would be fine to say. Both expressions are used here in the USA. I would say that if you had to choose, the most common would be "it cleared up". For example: "We were about to cancel the hike (or picnic or sailing or …..) but it cleared up and we had a wonderful day at the park. "The photographer was going to have us all go inside, but it cleared up and we were able to take the photos in the garden." "This morning, it looked like rain was coming, but then it cleared up and was sunny all afternoon." I hope that these examples help!

I would say “the sky is clear” and that means that it’s not cloudy anymore. I hope that helps