You can pass in a tag indicating the message you’re targeting, but I know of no chat client that only deletes the targeted message at this time. The target-msg-id tag gets passed through.
@target-msg-id=13ff63d1-b76e-48b3-89ff-fd5f8d49632b PRIVMSG #channel :/timeout user duration reason
>>>
@ban-duration=280;ban-reason=reason;room-id=118170488;target-msg-id=13ff63d1-b76e-48b3-89ff-fd5f8d49632b;target-user-id=17089325;tmi-sent-ts=1527178712589 CLEARCHAT #channel :user