The MSPs voted 99-11 with one abstention to exclude the Greens from a meeting of the Committee on Equality, Human Rights and Civil Justice.
It comes after she failed to declare her interest during a meeting of that committee in May of last year.
With the committee considering controversial gender recognition reforms, Ms Chapman had been questioning the chief executive of Rape Crisis. Scotland – but did not mention her previous employment as director of operations at the Edinburgh Rape Crisis Centre.
Holyrood’s Standards, Procedures and Public Appointments Committee ruled unanimously last week that by doing so, Ms Chapman had breached both the MSP code of conduct and legislation relating to MSP interests.
Standards committee coordinator Martin Whitfield said Ms Chapman’s actions meant there was “a lack of transparency” in her questioning.
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He said: “We live in a time where there is a lot of skepticism and mistrust of politicians.
“In order for us to challenge those perceptions, it behooves us to act with integrity and abide by the rules of the code of conduct.
“It is also incumbent on us, I think in certain circumstances, to exclude a member from Parliament proceedings where a member has not complied with the requirement to declare an interest.”
Green MSP Mark Ruskell said his party accepted the decision that Ms Chapman had breached the code of conduct, but “wrestled” with the decision to sanction her.
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He said that in previous cases where MSPs had not declared an interest, Parliament had not imposed any punishment.
Mr Ruskell said: “This case against Maggie Chapman relates to a former job that had long since ended at the time the article in business took place in this Parliament.
“So there was no way that Ms. Chapman would have benefited financially from the issue that was being discussed that day.”
The Green went on to express concern that the decision to sanction his colleague could set a precedent that leaves MSPs “financially tied to all of our previous employers for an indefinite period.”