The Messenger of Allah ﷺ used to pray witr with three rak'ahs. In the first he would recite: "Glorify the Name of Your Lord, the Most High" in the second: "Say: O you disbelievers!", and in the third: "Say: He is Allah, (the) One". And he would say the Qunut before bowing, and when he finished he would say: Subhanal-Malikil-Quddus (Glory be to the Sovereign, the Most Holy) three times, elongating the words the last time.  

أَنَّ رَسُولَ اللَّهِ ﷺ كَانَ يُوتِرُ بِثَلاَثِ رَكَعَاتٍ كَانَ يَقْرَأُ فِي الأُولَى بِ { سَبِّحِ اسْمَ رَبِّكَ الأَعْلَى } وَفِي الثَّانِيَةِ بِ { قُلْ يَا أَيُّهَا الْكَافِرُونَ } وَفِي الثَّالِثَةِ بِ { قُلْ هُوَ اللَّهُ أَحَدٌ } وَيَقْنُتُ قَبْلَ الرُّكُوعِ فَإِذَا فَرَغَ قَالَ عِنْدَ فَرَاغِهِ سُبْحَانَ الْمَلِكِ الْقُدُّوسِ ثَلاَثَ مَرَّاتٍ يُطِيلُ فِي آخِرِهِنَّ  

"The Messenger of Allah ﷺ used to recite: "Glorify the Name of Your Lord, the Most High;" in witr, in the second rak'ah he would recite: "Say: O you disbelievers!"; and in the third "Say: He is Allah, (the) One". And he only said the taslim at the end, and he would say- meaning after the taslim: Subhanal-Malikil-Quddus (Glory be to the Sovereign, the Most Holy)' three times."  

كَانَ رَسُولُ اللَّهِ ﷺ يَقْرَأُ فِي الْوَتْرِ بِ { سَبِّحِ اسْمَ رَبِّكَ الأَعْلَى } وَفِي الرَّكْعَةِ الثَّانِيَةِ بِ { قُلْ يَا أَيُّهَا الْكَافِرُونَ } وَفِي الثَّالِثَةِ بِ { قُلْ هُوَ اللَّهُ أَحَدٌ } وَلاَ يُسَلِّمُ إِلاَّ فِي آخِرِهِنَّ وَيَقُولُ يَعْنِي بَعْدَ التَّسْلِيمِ سُبْحَانَ الْمَلِكِ الْقُدُّوسِ ثَلاَثًا  

"The Messenger of Allah ﷺ used to recite: "Glorify the Name of Your Lord, the Most High;" in witr, in the second rak'ah he would recite: "Say: O you disbelievers!"; and in the third "Say: He is Allah, (the) One". And he only said the taslim at the end, and he would say- meaning after the taslim: Subhanal-Malikil-Quddus (Glory be to the Sovereign, the Most Holy)' three times." (Using translation from Nasāʾī 1701)   

كَانَ رَسُولُ اللهِ ﷺ يَقْرَأُ فِي الْوِتْرِ بِسَبِّحِ اسْمَ رَبِّكَ الْأَعْلَى وَفِي الرَّكْعَةِ الثَّانِيَةِ بِقُلْ يَا أَيُّهَا الْكَافِرُونَ وَفِي الثَّالِثَةِ بِقُلْ هُوَ اللهُ أَحَدٌ وَلَا يُسَلِّمُ إِلَّا فِي آخِرِهِنَّ وَيَقُولُ بَعْدَ التَّسْلِيمِ «سُبْحَانَ الْمَلِكِ الْقُدُّوسِ» ثَلَاثًا [273] خَالَفَهُ عَبْدُ الْعَزِيزِ بْنُ عَبْدِ الصَّمَدِ وَمُحَمَّدُ بْنُ بِشْرٍ  

“We asked ‘Aishah what the Messenger of Allah ﷺ used to recite in Witr. She said: ‘He used to recite: “Glorify the Name of your Lord the Most High,” [Al-A’la (87)] in the first Rak’ah, ‘Say: “O disbelievers!’” [Al- Kafirun (109)] in the second Rak’ah, and ‘Say: Allah is One’ in the third and the Mu’awwidhatain (Chapter 113, 114).’” (Using translation from Ibn Mājah 1173)   

سَأَلْنَا عَائِشَةَ بِأِيِّ شَيْءٍ كَانَ يَقْرَأُ رَسُولُ اللهِ ﷺ فِي الْوِتْرِ؟ فَقَالَتْ كَانَ يَقْرَأُ فِي الرَّكْعَةِ الْأُولَى بِسَبِّحِ اسْمَ رَبِّكَ الْأَعْلَى وَفِي الثَّانِيَةِ بِقُلْ يَا أَيُّهَا الْكَافِرُونَ وَفِي الثَّالِثَةِ بِقُلْ هُوَ اللهُ أَحَدٌ وَالْمُعَوِّذَتَيْنِ