Yes, you can say that. It means "I went for a run." Strictly speaking it is not the past continuous, which would be "I was running." It is the past tense of "go" + the gerund of "run."
Other examples:
I went to shop ==> I went shopping
I went to fish ==> I went fishing
I went to fly (as in flying a lightweight aircraft) ==> I went flying
I went to ski ==> I went skiing.
I went to swim ==> I went swimming.
You usually use this construction for verbs denoting a hobby or an active activity.
So you can't say: I went to sleep XXX I went sleeping.
I went to eat XXX I went eating (sounds funny).