One person is writing a letter to his friend ,who had recommended this trip to him, about trip and following sentence is from that letter.
We had a fantastic time in South Africa.
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The reason we use the indefinite article in "We had a fantastic time in South Africa" is the same reason we use the indefinite article in "We had a fantastic experience", "It was a fantastic occasion", "a fantastic trip", "a fantastic holiday/vacation".
On the other hand, we would say "we had fantastic fun" or (maybe more likely) "we had great fun". We wouldn't say "a great fun".
In some contexts, "time" (like "fun") is a mass noun (uncountable): "I wish we had more time", "we spent a lot of time on it", "we don't have time".
In other contexts, "time" (like "occasion") is a countable noun: "we'll have to do it another time", "I've been there many times", "we had a good time".
The fact that "fun" is a mass noun means that the indefinite article isn't used, whereas with "time" (when it means "occasion"/"experience") the indefinite article must be used in sentences such as "we had a fantastic time".