In the Supergirl episode "Better Angels" we have the following exchange between Kara (Supergirl) and her sister:
Alex: Once you're in space, there's no atmosphere. There's no gravity. You wouldn't be able to generate thrust, you wouldn't be able to breathe, you wouldn't be able to get back.
Kara: There is no other way.
My question is, why was Supergirl unable to breathe in space?
why could Supergirl not be able to breathe in space?
Because no-one can...there's no air.
She can't breathe in space unless she stores solar energy and holds her breath.
In the modern version of Superman (in the comics at least until the next version), Superman's sight, stamina and breath powers have been substantially reduced, and the character was also shown as requiring an oxygen mask for prolonged travel in space or underwater.
The same would apply to Supergirl.
I suspect though you are asking why Supergirl became unconscious and had to be rescued.
Well, she'd just lifted the 1 million ton Fort Rozz into orbit and beyond...that would have expended a...ahem...superhuman amount of energy which would have depleted her reserves. Plus the air is essentially too thin to breathe over 10,000 meters and Earth orbit is substantially higher than that.
So, she ran out of energy and breath and fell unconscious.
Well since superman has done things like held a miniature blackhole in the palm of his hand or picked up all of earth's nuclear missiles and threw them in the sun or when he pulled whole planets around for supergirl to be so weak only thing I can think of is that she was on earth for a shorter amount of time with the added fact there's plenty of proof stating that female kryptonions are a bit weaker but still she should have been able to atleast fly back
