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The correct way to perform Witr is to pray 3 raka'ah only, as it has been proven as a sunnah of Rasulullah Sallallho 'Alyhi Wasallam and an act proven through the actions of Rasulullah Sallallaho 'Alyhi Wasallam and the Sahaba Kiram Rizwanullah Ta'ala 'Alyhim Ajmaeen. Hazrat Abdullah Bin Masood RaziAllah Ta'ala 'Anhu said:
Like salatul-Maghreb, salatul-Witr also has 3 raka'ah.
Hazrat Ayesha RaziAllah Ta'ala Anha says that:
Rasulullah Sallallho 'Alyhi Wasallam used to perform (lead) 3 raka'ah of Witr.
In other narrations, it has been mentioned that in the first raka'ah Rasulullah Sallallaho 'Alyhi Wasallam would read surah al-Ala (سَبِّحِ ٱسۡمَ رَبِّكَ ٱلۡأَعۡلَى), in the second raka'ah would read surah al-Kafiroon and in the third raka'ah would read surah al-Ikhlas. This proves the ruling of the 3 raka'ah of Witr in light of the ahadees of Rasulullah Sallallaho 'Alyhi Wasallam.
The second issue is whether Witr is performed with one salam and that salam shall not be performed at the second raka'ah mark. Hazrat Ayesha RaziAllah Ta'ala Anha says that:
Rasulullah Sallallaho 'Alyhi Wasallam would perform 3 raka'ah of Witr and would not perform salam until the end.
There are other narrations from Hazrat Abdullah Ibnay-Abbas RaziAllah Ta'ala Anhu, Hazrat Ayesha RaziAllah Ta'ala Anha and other sahaba kiram that Rasulullah Sallallaho 'Alyhi Wasallam did not perform salam at the second raka'ah mark, rather he performed it at the end (of the third raka'ah). Therefore, Witr salah shall be prayed with one salam and with completing three raka'ah.
As far as reading qunoot before ruku' in the third raka'ah is concerned, there are several books of hadees including al-Juz-ul-Yadain (Imam Bukhari), Masnad Ibn-e-Abi-Shaybah, Mustadrak al-Hakim, Mu'jamul-Tabrani, Mu'jamul-Zawaid, etc. where ahadees have been narrated regarding this, Hazrat Abdullah Ibnay-Masood RaziAllah Ta'ala Anhu says:
Rasulullah Sallallaho 'Alyhi Wasallam used to read surah al-Ikhlas in the last raka'ah of Witr, then he raised his hands and read qunoot before performing the ruku'.
This narration and other similar narrations have been documented in Sunan al-Tirmidhi, Sunan an-Nasai, Musnad Ahmed Ibnay-Hambal, Mustadrak al-Hakim and other books of hadees.
In light of the above ahadees the following points have been proven:
1- Witr is with 3 raka'ah only
2- Witr is performed with one salam and salam shall not be performed with 2 raka'ah
3- Qunoot shall be read before performing ruku' in the 3rd raka'ah
4- Raising the hands before going into ruku' of the third rakah has also been proven in light of the hadees from al-Juz-ul-Yadain (Imam Bukhari)
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