The Prophet ﷺ would recite in the two units of prayer after which he prayed Witr, "Glorify the name of your Lord, the Most High" [Ala 87:1] and "Say, you disbelievers" [Kafirun 109:1]. And in the Witr he would recite "Say, He is Allah, the One" [Ikhlas 112:1], "Say, I seek refuge with the Lord of the daybreak" [Falaq 113:1], and "Say, I seek refuge with the Lord of mankind" [Nas 114:1].
أن النبي ﷺ كان يقرأ في الركعتين التي يوتر بعدهما: ب {سبح اسم ربك الأعلى} و{قل يأيها الكفرون} ويقرأ في الوتر: ب {قل هو الله أحد} و {قل أعوذ برب الفلق} و {قل أعوذ برب الناس}.
Daraqutni (2/34-35) and Hakim (1/305), and from him Bayhaqi (3/37), narrated it from Husayn bin Ismail, who said, Abu Hatim Razi told us, Saeed bin Afir told us, Yahya bin Ayub told us, from Yahya bin Saeed, from Amra bint Abdul-Rahman, from Ayesha, and he mentioned it. Hakim said, "Sahih according to the standard of the two Shaykhs."Its chain of transmission is hasan, because Yahya bin Ayub Ghafiqi is disputed, though his hadith is hasan. Bukhari, Abu Dawud, and others deemed him reliable, while Nasai and Ibn Saad criticized him. Bukhari cited him as a corroborating witness, and Muslim relied on him as evidence. Ibn Hibban graded it sahih (2432) and narrated it through another route from Saeed bin Afir, similarly. What appears from her saying, "the one with which he performed Witr after them," is that he prayed a rakat separate from the two.But Daraqutni, Hakim, and Bayhaqi narrated it through another route from Saeed bin Abu Maryam, from Yahya bin Ayub, with the wording, "and he used to recite in the third..." and he mentioned the rest of the hadith. Hakim said, "It is sahih according to the standard of the two Shaykhs, though they did not include it. Saeed bin Afir is, without dispute, the imam of the people of Egypt, and he has given the hadith in an explained, corrected form, indicating that the rakat which constitutes the Witr is a separate one, distinct from the two rakats before it."I say, there is no need to declare anyone mistaken, for heﷺ may have prayed it separated on one occasion and connected on another, as is established in the sahih hadiths. This chain of transmission is the soundest through which the hadith of Ayesha has been narrated.Tirmidhi alluded to it (463) after narrating it through the route of Khaseef, as did Abu Dawud (1424), Ibn Majah (1173), Ahmad (25906), and Hakim (2/520-521), all of them through the route of Khaseef, from Abdul-Aziz bin Jurayj, who said, "I asked Ayesha, mother of the believers, with what did the Messenger of Allahﷺ perform Witr?" She replied, and he mentioned something like the hadith of Ubayy bin Kaab, adding that in the third rakat, after "Say, He is Allah, the One" [Ikhlas 112:1], he recited the two surahs of refuge.Tirmidhi said, "hasan gharib." Hakim said, "Its chain of transmission is sahih." I say, rather its chain of transmission is daif, due to the weakness of Abdul-Aziz bin Jurayj Makki, father of Abdul-Malik. Bukhari said, "He is not corroborated in his hadith." Ajli said, "He did not hear from Ayesha, and Khaseef erred by stating explicitly that he heard from her." Daraqutni said, "He is unknown."Hafiz said in Nataij Afkar (p. 512), "Perhaps his grading it hasan was based on the aforementioned route, since Hafiz graded the route of Yahya bin Ayub Ghafiqi as hasan." Likewise, Nawawi acknowledged Tirmidhi's grading it hasan in Khulasa (1883). The two chains of transmission strengthen one another, so there is nothing objectionable in reciting the two surahs of refuge in Witr.Imam Ahmad was asked about reciting the two surahs of refuge in Witr, and he said, "Why should he not recite them?" But what we prefer is that one recite in Witr "Glorify" [Ala 87:1], "Say, O disbelievers" [Kafirun 109:1], and "Say, He is Allah, the One" [Ikhlas 112:1]. Likewise, Malik was asked about the recitation in Witr, and he said, "People have always recited the surahs of refuge in Witr, and I recite them in Witr."On this subject is what is narrated from Abu Musa, that he led his companions in prayer while traveling from Makkah to Madinah. He prayed Isha as two rakats and gave the taslim. Then he stood and recited a hundred verses from Surah Nisa in one rakat. This was objected to, so he said, "I have not failed to place my foot where the Messenger of Allahﷺ placed his foot, and to do just as the Messenger of Allahﷺ did."Nasai (1728), Abu Dawud Tayalisi (514), Ahmad (19760), and Bayhaqi (3/25) all narrated it through the route of Asim bin Sulayman Ahwal, from Abu Majliz, who said, "Abu Musa led his companions in prayer," and he mentioned it. There is a break in this chain between Abu Majliz, who is Lahiq bin Humayd, for he did not meet Abu Musa, who died in the year 50 AH, since Ali bin Madini said, "He did not meet Samura, who died in the year 58 AH, nor Imran, who died in the year 52 AH." End of his statement.Yahya bin Main said, "He did not hear from Huzaifa."