Professor Alice Brown had already won the unanimous backing of a reappointment panel of MSPs when they considered it earlier this year.
The ombudsman's position, which was set up in 2002, provides a one-stop shop for individuals making complaints about maladministration or service failure in a wide range of organisations providing public services in Scotland.
She usually considers complaints which have already been looked into by the organisations concerned.
These include councils, housing associations, the NHS, the Executive, colleges and universities.
Brown earns in the region of 85,000 to 90,000 a year and is supported in her work by three part-time deputy ombudsmen and 38 members of staff.
Putting forward a motion for her to serve a second term, which was agreed by 113 votes to one with two abstentions, reappointment committee member John Scott acknowledged concerns about the quality and the length of time taken for reports to be published.
He said the issue had been discussed with Brown, who gave assurances that problems would be addressed.
Scott, the Tory MSP for Ayr, said the budget for the ombudsman had been increased by 20 per cent, which will allow for an additional seven staff to be employed. And he said that, although 14,000 cases have been dealt with, only 20 complaints have been received about the quality of the ombudsman's work.
"I have no doubt at all that the ombudsman is fully committed to providing a first-class service to the public and ensuring that all public authorities learn from the complaints," he added.
The SNP's John Swinney said he would be backing the reappointment, but also raised concerns about the operation of the ombudsman service.
Swinney, the MSP for Tayside North, challenged the amount of time taken to process some cases and questioned the "ethos" of the organisation, which he claimed was not strong enough in its "critique" of public services.
"What concerns me is the fact that if we are going to set up a Scottish Public Services Ombudsman we must be absolutely confident as MSPs that the ombudsman service is going to be robust and tough with public organisations," he said. "I'm very uneasy about whether that's the case at present. I hear the reassurances Mr Scott has given on this point to Parliament and I look with real enthusiasm to ensure that those issues will be addressed by the ombudsman in her second term of office."
Before being appointed as ombudsman, Brown was the vice-principal and co-director of the Institute of Governance at Edinburgh University.