I gambled with 9000 then I won 12000. Now I feel this is haram. What should I do?

Praise be to Allah, the Lord of the Worlds; and may His blessings and peace be upon our Prophet Muhammad and upon all his Family and Companions.

Making a bet between two people or more with a sum of money from each side so that one will lose his money and the other will win is Haram as stated by Ibn Rushd since it constitutes a form of gambling. This is the opinion of all Muslim scholars.
Therefore, it is the inquirer's duties to repent to Allah and to get rid of the money he received from bets, i.e. three thousand dollars. In other words, he has to spend such amount on behalf of the Muslim commons, not as Sadaqa.
Here, we remind you of the following Prophetic Hadith: "A servant of Allah will remain standing on the Day of Judgement till he is questioned about his youth, how he spent it, and about his knowledge and how he utilized it, and about his wealth from where he acquired it and in what activities he spent it; and about his body and how he consumed it" [ al-Tirmizi, al-Albani regarded it as sound Hadith]
Allah knows best.