You can use your query as a subquery:
SELECT *
FROM table
WHERE id IN (SELECT MAX(id) AS id
FROM table
WHERE final=0 AND username='$username' AND active=1
GROUP BY unique_id)
ORDER BY order_number
or, if idnot unique, use JOIN:
SELECT t1.*
FROM table AS t1
JOIN (SELECT MAX(id) AS max_id, unique_id
FROM table
WHERE final=0 AND username='$username' AND active=1
GROUP BY unique_id
) AS t2 ON t1.unique_id = t2.unique_id AND t1.id = t2.unique_id
ORDER BY order_number
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