It can be done if the fluid level is deep enough, but it is not advisable from a sanitation perspective in my opinion. I’d just watch the fermentation and give it a few days after the krausen drops and the beer clears. Otherwise drawing off some to put in a measuring tube with the hydrometer is the preferred approach. Small batch brewing has its obstacles, such as this, but it will turn out fine for you, I am sure.
Cheers!