The attacks come days after 29-year-old Salih Khater, who is from the city, was arrested after a car collided with cyclists and pedestrians and crashed into a security barrier in Westminster.
Officers were called to the Masjid Qamarul Islam mosque on Fosbrooke Road, Small Heath, at around 10pm on Wednesday, and to the Al-Hijrah mosque on Hob Moor Road 20 minutes later.
West Midlands Police said it had recovered some ball bearings which smashed windows during evening prayers.
They appeared to have been fired from a substantial catapult, officers added.
Police are patrolling the area to reassure residents, and say a motive is unclear at this stage.
A trustee of Birmingham Central Mosque, Nassar Mahmood, has said Muslims are facing “unprecedented” levels of Islamophobia at present.
Speaking after what happened in Westminster on Tuesday, he said women are particularly affected because their style of dress makes them “quite visible”.
He has asked the media not to speculate on why the Westminster incident happened, adding: “We would ask you to be cautious of apportioning blame to the Muslim community.
“We are shocked and saddened by this just the same as everybody else.”
Anyone with information on the mosque attacks is asked to call 101.