My baby was born with hypotonia. Physio work wonders to rehabilate muscles all over his body. But his face still has very low tone. What can I do?

Oral motor therapy. Depending on the extent of physical therapy being given and the severity of your baby's hypotonia, occupational therapy and even speech therapy (they can do oral motor therapy to help with feedings) may be needed. Gentle massage and range of motion exercises also help the whole body and increase bonding. Make sure you also get some rest for yourself!
See a geneticist. If your baby hasn't already seen a specialist in genetics, i would strongly recommend it. Sometimes genetic tests can help determine the cause of the hypotonia which may help with treatments and therapies as well.
Diagnosis? . Are you seeing a pediatric neurologist? What is the baby's diagnosis? Please follow up with you pediatrician soon to help you pursue a diagnosis, which will lead you to a "prognosis" ( how we expect this problem will progress) as well as a treatment plan. Very close developmental follow up is warranted! Best of luck! .
Suggestions. I'm glad that you got your baby right in to early intervention services & that (s)he's responding to therapy. You may be able to see a geneticist & developmental/behavioral pediatrician through ei, if you haven't done so already, to try to find out what caused this & what it means for future development. Ot's & slt's often work together, since the same muscles are used for eating & talking.
Suck and swallow. For babies the best facial exercise is suck and swallow as well as smiling and facial expression. Just play with him and help him feed and be cautious and allow time to help.