Witr prayer is part of the night prayer, but there is still a difference between them.
Shaykh Ibn Baaz (may Allaah have mercy on him) said:
Witr is part of the night prayer, and it is Sunnah and it is the end of the night prayer, one rak’ah with which one concludes the night prayers at the end of the night, or in the middle of the night, or at the beginning of the night after ‘Isha’ prayer. You pray whatever you can, then you conclude it with one rak’ah. End quote.
Fataawa Ibn Baaz, 11/309
Shaykh Ibn ‘Uthaymeen (may Allaah have mercy on him) said:
The Sunnah – both in word and in deed – distinguishes between the night prayers and witr prayer. The scholars also distinguished between them with regard to the ruling and the way in which they are done.
With regard to differentiation made in the Sunnah, according to the hadeeth of Ibn ‘Umar (may Allaah be pleased with him), a man asked the Prophet (peace and blessings of Allaah be upon him): How are the night prayers done? He said: “Two by two, then when you fear that dawn is about to break, pray Witr with one rak’ah.” Narrated by al-Bukhaari. See al-Fath, 3/20.
With regard to the way in which the Prophet (peace and blessings of Allaah be upon him) differentiated between them in his actions, according to the hadeeth of ‘Aa’ishah (may Allaah be pleased with her): The Prophet (peace and blessings of Allaah be upon him) used to pray when I was lying down across his bed. When he wanted to pray Witr, he would wake me up and I would pray Witr. Narrated by al-Bukhaari. See al-Fath, 2/487. Also narrated by Muslim (1/51) with the wording: “He used to offer his prayers at night when I was lying in front of him.” Then when only Witr was left, he would wake her up and she would pray witr. And Muslim also narrated (1/508) that she said: The Messenger of Allaah (peace and blessings of Allaah be upon him) used to pray thirteen rak’ahs at night, five of which were witr, in which he would not sit except at the end. And he narrated from her (1/513) that when Sa’d ibn Hishaam said to her: “Tell me about the Witr of the Messenger of Allaah (peace and blessings of Allaah be upon him),” she said: “The Prophet (peace and blessings of Allaah be upon him) used to pray nine rak'ahs during which he would not sit except in the eighth rak’ah, when he would remember Allaah and praise Him and call upon Him, then he would get up without saying the salaam, then he would stand and pray the ninth rak’ah, then he would sit and remember Allaah (dhikr) and praise Him and call upon Him, then he would say a tasleem that we could hear.”
With regard to the way in which the scholars differentiated between the ruling on witr and the night prayers, the scholars differed as to whether Witr is obligatory. Abu Haneefah was of the view that it is obligatory, and this was narrated from Ahmed in al-Insaaf and al-Furoo’. Ahmad said: Whoever fails to pray Witr deliberately is a bad man whose testimony should not be accepted.
The well known view in our madhhab is that witr is Sunnah. This is the view of Maalik and al-Shaafa’i.
With regard to the night prayers, there is no such scholarly dispute. In Fath al-Baari (3/27) it says: I have not seen anyone narrate the view that it is obligatory except for some of the Taabi’een. Ibn ‘Abd al-Barr said: Some of the Taabi’een held an odd view and said that qiyaam al-layl is obligatory, even if it is done only for the length of time that it takes to milk a sheep. But the view of the majority of scholars is that it is recommended. End quote.
With regard to the scholars’ differentiating between the ways in which witr and the night prayers are done, our Hanbali fuqaha’ have clearly stated that they are done differently. They said: The night prayers are done two by two, and they said concerning witr: witr may be prayed with five, or seven, rak’ahs, in which one does not sit except in the last one. If a person prays witr with nine rak’ahs, he should sit immediately after the eighth rak’ah and recite the tashahhud, then he should stand up before saying the salaam and do the ninth rak’ah, then he should say the tashahhud and the salaam. This is what was stated by the author of Zaad al-Mustaqni’. End quote.
Majmoo’ Fataawa Ibn ‘Uthaymeen, 13/262-264.
Thus it is clear that witr prayer is part of the night prayers, but it differs from them in some minor details such as how it is done.
And Allaah knows best.