I experienced this same problem last year. I cleaned the 12 volt connections and have'nt had a problem since. It could have been air in the gas line though, I didn't give it time to develop a pattern of not igniting.
First go outside, open your water heater inspection door and watch as it attempts to re-light; you may discover the problem visually. (Strong spark?) While your cleaning the 12 volt connections make sure you don't have insect nests or webs causing a problem. But, I doubt that that is your problem since you can ignight by shutting system down and then turning back on.
Let us know your fix, we all learn together.
"If everything seems to be going well, look around, you've obviously overlooked something."