How did the Prophet (peace be upon him) pray the night prayer without sitting between rak'ahs, then pray two rak'ahs sitting?

Perhaps you are asking about the hadith narrated by Aisha (may Allah be pleased with her) concerning the description of the Prophet's Witr prayer (peace and blessings be upon him). It is stated in Al-Nawawi's commentary on Sahih Muslim: "Her saying: 'He would pray thirteen rak'ahs at night, performing Witr with five of them, not sitting except in the last one'," and in another narration: "He would give the salutation after every two rak'ahs," and in another: "He would pray four, then four, then three," and in another: "eight rak'ahs, then perform Witr with one rak'ah," and in another: "ten rak'ahs and perform Witr with one prostration."

Al-Nawawi said: "The correct view is that the Prophet (peace and blessings be upon him) performed these two rak'ahs after Witr while sitting, to show the permissibility of praying after Witr, and to show the permissibility of performing supererogatory prayers while sitting. He did not consistently do so; rather, he did it once, twice, or a few times."

Imam Ibn al-Qayyim spoke about these two rak'ahs, saying: "This has been a source of confusion for many people, who thought it contradicted his (peace and blessings be upon him) saying: 'Make the last of your prayer at night Witr.' Imam Malik (may Allah have mercy on him) rejected these two rak'ahs, and Ahmad said: 'I do not do it, but I do not forbid it.' A group of scholars said: 'He only performed these two rak'ahs to show the permissibility of prayer after Witr, and that his action does not interrupt supererogatory prayers.' They interpreted his saying: 'Make the last of your prayer at night Witr' as a recommendation, and the prayer of two rak'ahs after it as permissible.

The correct view is to say: These two rak'ahs are like a Sunnah, complementing the Witr prayer. Indeed, Witr is an independent act of worship, especially if its obligation is upheld. So, the two rak'ahs after it are like the Sunnah of Maghrib prayer after Maghrib, for Maghrib is the Witr of the day, and the two rak'ahs after it complete it. Similarly, the two rak'ahs after the Witr of the night."

Based on the above, the two rak'ahs after Witr are confirmed to have been performed by the Prophet (peace and blessings be upon him), but some scholars interpreted them as an indication of the permissibility of supererogatory prayers after Witr. They said that it is preferable to end the night prayer with Witr, in compliance with his (peace and blessings be upon him) command, as stated in the authentic hadith.