Neither the PM nor the president were in the buildings at the time.
Hundreds of thousands descended on the capital Colombo, calling for Mr Rajapaksa to resign after months of protests over economic mismanagement.
Mr Rajapaksa will step down on 13 July. PM Wickremesinghe has agreed to resign.
The speaker of parliament said the president decided to step down "to ensure a peaceful handover of power" and called on the public to "respect the law".
The announcement triggered an eruption of celebratory fireworks in the city.
