Yogurt as well as ice cream and other soft foods can be eaten when you have the Invisalign on your teeth.
However it's better and best to remove the Invisalign before eating any yogurt or other soft foods such as ice cream.
Removing the Invisalign before eating any yogurt or ice cream or other soft foods will keep the Invisalign cleaner and so you won't have to clean it as often.
So I would recommend removing the Invisalign and then eating the yogurt or other soft foods and then put them back in after you brush your teeth.
So while you can eat yogurt with the Invisalign in you should remove the Invisalign first before eating yogurt.