Hi Verbena37,
Sorry to hear that you've both had a difficult time this morning but please be reassured that every one at Interhigh (staff and pupils) are very laid back and fluid with adapting to changes in your personal circumstances and one will be upset that your son didn't make it to class today.
Do you have a parent login yet? If you do then that's where you can go to log an absence. There's no immediate deadline to do it (10-14 days or something!) If you don't have a parent login then email or ring admin and let them know that he wasn't well. They'll not pry and I'm sure they'll be very relaxed and understanding about it.
Your son doesn't need to worry about what the teacher or his class mates will think. Very often students (sometimes teachers!) have blackboard or internet connection troubles and don't turn up to or disappear halfway through a lesson. No one ever seems to ask where you've been or what happened. Tomorrow when he logs in, it will all be as usual 
Our 1st Interhigher joined this time of the school year and it is a hard time for them to join. The classes will be revising subjects covered during the past school year in preparation for the end of year tests and it can seem a little alienating at times. Come September everyone will be on the same page again and he'll feel a lot more at ease. It's also quite stressful for them to figure out the software, the structure of the school and flow of the lessons and his new teachers for the first few weeks but I'm sure if he can give it a shot for a while, he'll soon settle in.
I don't know your circumstances but if you think it would help him, maybe you could slowly build up the number of days he attends as he settles in until he manages the full week? Please don't worry at home by yourselves. Reach out to the staff at Interhigh and I'm sure they'll be more than happy to help you. They'll want to see your son settled and happy as much as you do 
I have rambled on and I've typed this on my phone so apologies for grammar and spelling!
Hoping you and your son can put this morning behind you. We all have those mornings don't we 
Socks