A duʿāʾ recommended to be recited in the Qunūt of Ṣalāt al-Witr (as part of Ṣalāt al-Layl), as reported by the Aʾimmah (as) and originating from the Prophet (Ṣaww), has been recorded in multiple sources:
The text of the duʿāʾ itself is as follows:
حَدَّثَنَا قُتَيْبَةُ، حَدَّثَنَا أَبُو الأَحْوَصِ، عَنْ أَبِي إِسْحَاقَ، عَنْ بُرَيْدِ بْنِ أَبِي مَرْيَمَ، عَنْ أَبِي الْحَوْرَاءِ السَّعْدِيِّ، قَالَ قَالَ الْحَسَنُ بْنُ عَلِيٍّ رضى الله عَنْهُمَا عَلَّمَنِي رَسُولُ اللَّهِ صلى الله عليه وسلم كَلِمَاتٍ أَقُولُهُنَّ فِي الْوِتْرِ :
اللَّهُمَّ اهْدِنِي فِيمَنْ هَدَيْتَ وَعَافِنِي فِيمَنْ عَافَيْتَ وَتَوَلَّنِي فِيمَنْ تَوَلَّيْتَ وَبَارِكْ لِي فِيمَا أَعْطَيْتَ وَقِنِي شَرَّ مَا قَضَيْتَ فَإِنَّكَ تَقْضِي وَلاَ يُقْضَى عَلَيْكَ وَإِنَّهُ لاَ يَذِلُّ مَنْ وَالَيْتَ تَبَارَكْتَ رَبَّنَا وَتَعَالَيْتَ.
Translation:
Al- Ḥasan bin ʿAlī [may Allah be pleased with him] said: ‘Allah’s Messenger (Saww) taught me some words to say during Al-Witr:
‘O Allah guide me among those whom You have guided, grant me ʿĀfiyah (wellbeing and safety) among those whom you have granted it, befriend me and be my ally among those whom You have befriended and allied Yourself with, bless me in what You have granted, and save me from the evil of what You have decreed. Indeed You pass all decrees, and none can pass decree over You. Indeed he whom You have befriended and allied with cannot be humiliated; Blessed are You, our Sustaining and Nurturing Lord, and Exalted You are’!
Source: Al-Ṣadūq, Shaykh Abū Jaʿfar Muḥammad bin ʿAlī bin al-Ḥusain bin Mūsā Ibn Bābawayh al-Qummī. Man Lā Yaḥḍuruhū al-Faqīh. Ed.ʿAlī Akbar al-Ghaffārī. Muʾassasat al-Nashr al-Islāmī al-Tābiʿah li Jamāʿat al-Mudarrisīn bi Qum al-Musharrafah, Qum, 5th ed., 1429 AH., vol. 1, p. 487. [Narration # 1404 – 1]. (https://lib.eshia.ir/11021/1/487).
Imām ʿAlī bin Mūsā al-Riḍā (as) is also reported as having made the recitation of this duʿāʾ in the Qunūt of Witr his regular practice.
Source: Al-Ṣadūq, Shaykh Abū Jaʿfar Muḥammad bin ʿAlī bin al-Ḥusain Ibn Bābawayh al-Qummī. ʿUyūn Akhbār al-Riḍā. Manshūrāt al-Sharīf al-Raḍī, Qum, 1st ed., 1378., vol. 2, p. 195. [Narration # 5]. (https://lib.eshia.ir/14032/1/195).
See also: Al-Malāyerī, al-Ḥājj Shaykh Ismāʿīl al-Muʿizzī. Jāmiʿ Aḥādīth al-Shīʿah fī Aḥkām al-Sharīʿah. Compiled under the auspices and supervision of al-Imām Āyatullāh al-ʿUẓmā al-Ḥājj al-Sayyid Ḥusayn al-Ṭabāṭabāʾī al-Burūjerdī. Intishārāt Wāṣif Lāhījī, Qum, 1433 AH, vol. 5, pp. 579–580. [Narration no. 8684 (15)]. (https://lib.eshia.ir/10565/5/322).
Reference for this in Sunni sources: Abu Khaliyl (Tr.). English Translation of Jāmiʿ At-Tirmidhī. (Compiled by Imām Hāfiẓ Abū ʿEisā Mohammad Ibn ʿEisā At-Tirmidhī. Ed. Hāfiẓ Abu Tāhir Zubair ʿAlī Za’i. Darussalam, Riyadh, 2007 CE., vol. 1, pp. 468-469. [Ḥadīth # 464]. Jami` at-Tirmidhi 464 https://sunnah.com/tirmidhi:464.