The Messenger of Allah ﷺ used to perform the Witr prayer with three units. In the first he would recite "Glorify the name of your Lord, the Most High" [Ala 87:1], in the second "Say, O you who disbelieve" [Kafirun 109:1], and in the third "Say, He is Allah, the One" [Ikhlas 112:1]. He would make the qunut supplication before bowing, and when he finished he would say upon completion, "Glory be to the King, the Holy," three times, prolonging the last of them.
أخبرنا علي بن ميمون قال حدثنا مخلد بن يزيد عن سفيان عن زبيد عن سعيد بن عبد الرحمن بن أبزى عن أبيه
أن رسول الله ﷺ كان يوتر بثلاث ركعات كان يقرأ في الأولى بسبح اسم ربك الأعلى وفي الثانية بقل يا أيها الكافرون وفي الثالثة بقل هو الله أحد ويقنت قبل الركوع فإذا فرغ قال عند فراغه سبحان الملك القدوس ثلاث مرات يطيل في آخرهن
[Sahih] Ibn Majah reported it in the Book of Establishing the Prayers, chapter on what has been said about qunut before and after ruku, hadith no. 1182, from Ali bin Maymun, with this wording. It is also found in Al-Kubra, hadith no. 1432, and Diya included it in Al-Mukhtarah.Sufyan Thawri was followed by Fitr bin Khalifa, as found in Daraqutni, 2/31, hadith no. 1644.