Did you have any monitoring on the server (e.g. munin or similar) that you could check for the time in question?
What, roughly, is the spec of your server? That's enough students to wipe out a small server (as panic sets in and they start hitting refresh it just spikes and the machine goes down).
I suggest you read - http://docs.moodle.org/25/en/Performance_recommendations
We have the httpd logs, which our server admin says don't seem to indicate a server outage, and the Moodle Log, which I checked. The Moodle log indicates a seven minute gap in the entries, followed by three minutes with 30-40 entries per minute (I'm seeing periods where we get as many as 100 entries per minute without a gap), followed by a three minute gap.
Without any useful measurements I doubt you will get to the bottom of this. I would advice installing munin (https://help.ubuntu.com/12.04/serverguide/munin.html) so you might get a clue if it happens again. This logs all sorts of parameters over time - so you'll see if you ran out of RAM etc.. Also (but not as a substitute) think about Google Analytics or similar.
If you haven't done so already, you need to attend to Apache and MySQL tuning. Out of the box, Apache will burn up all your memory and MySQL is generally far too conservative. If this is wrong then the number of users you have could conceivably overwhelm the server.
You could do some load testing with something like JMeter (http://docs.moodle.org/dev/JMeter) but that can be tricky.