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.
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