Reference : Hisn al-Muslim 172

اللّهُمَّ صَيِّـباً نافِـعاً
Allāhumma ṣayyiban nāfi`a.

O Allah, (bring) beneficial rain clouds.

Reference:
Al-Bukhari, cf. Al-Asqalani, Fathul-Bari 2/518.

Chapter: When it rains