No, your suggested sentence is not natural. In the context of separation from one's spouse, we only use:
They (the couple) are separated.
She has separated from her husband.
She is separated from her husband.
He has separated from his wife.
He is separated from his wife.
And of course, these days (in many countries), it's just as possible for a wife to be separated from her wife and a husband to be separated from his husband.
If you said "I separated him from his wife" or your example sentence, I would assume the married couple were having a physical fight and you stepped between them to separate them by physical distance, nothing to do with their marital status.
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