The beam hung down, just missing a glass panel, and was left swinging over the seats of Conservative MSPs.
First Minister's Questions was postponed and votes on earlier debates will take place at a future session.
The beam was removed on Thursday evening and an inspection will be carried out on Friday morning.
The parliament will await advice from structural engineers before the chamber is reopened.
An urgent investigation was launched by parliament safety officers into the cause of the incident.
The section where the beam fell is normally occupied by Tory MSPs, but there were few members listening to the debate from there at the time.
The press gallery was also cleared.
Prior to the cessation of business, Deputy Presiding Officer Murray Tosh suspended proceedings while the safety situation was assessed.
Tory MSP John Scott, who has a civil engineering degree, said: "There has been a serious structural failure in one of the trusses that supports the roof of the debating chamber.
"In my view it's essential that for the structural integrity of the building to be maintained, it not only needs to be repaired but the whole of the remaining structure needs to be thoroughly checked and inspected before anyone re-enters the chamber."
A Scottish Parliament spokesman said structural engineers gave their professional advice, before the presiding officer decided to abandon business for the day.
There was huge controversy over the cost of the parliament building, which was designed by the late Catalan architect Enric Miralles.
However, an inquiry conducted by Lord Fraser into the spiralling cost found that no one person was to blame.
The building was officially opened by the Queen in October 2004 and has won a number of architectural awards.
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