When to make the Istikhaarah Supplication
Question: Is the istikhaarah supplication to be made in the prostration (position during the istikhaarah prayer) or after completing the (istikhaarah) prayer?
Response: The istikhaarah supplication is to be done upon completing the two units of (istikhaarah) prayer, as the Prophet (sal-Allaahu ‘alayhe wa sallam) said:
«…then let him pray two supererogatory units [two rak’ah naafilah] of prayer and after which he should supplicate…» [From the hadeeth of Jaabir ibn ‘Abdullaah (radhi-yAllaahu ‘anhu) as transmitted by al-Bukhaaree]
…and then he (sal-Allaahu ‘alayhe wa sallam) mentioned the (istikhaarah) supplication.
Shaykh Ibn `Uthaymeen
Fataawa al-Mu`aasarah – Page 392 source: fatwaonline.com