Hi L.,
I've been in your situation with my older daughter. When she was from about 3-5 years old, she, too, experienced what my doctor called night terrors. They are not fully awake when this is happening. At first I tried to console her, but to no avail. Then I learned that it was best to let her cry, and hold her if she wasn't thrashing around. Like you experienced, sometimes she would go back to sleep within seconds, other times it took a few minutes.
The good news is that not only will he probably not remember any of these night terrors (my daughter definitely didn't remember anything), there is also no emotional impact afterwards. It is like they are dreaming. It is also better that these are happening within an hour or two after he goes to sleep, so you can at least anticipate them more around that time. My daughter usually never had one past 10 or 11 o'clock, which was before or right at our bedtime.
My daughter's pediatrician told me that they usually outgrow these by the time they are in Kindergarten or not long after that. My daughter is now in third grade and is a very sound sleeper and rarely wakes up at night except to occasionally use the bathroom.