Around 15 demonstrators carrying "Atos Kills" posters invaded a constituency surgery in Sturgeon's Glasgow Southside seat on Friday to demand an end to the deal.
The peaceful protest ended after police were called to the Larkfield Centre in Govanhill but there were no arrests.
Sturgeon personally welcomed Atos as an official sponsor of Glasgow 2014 last year, calling the French IT giant's involvement "a significant step forward for the Games".
The company will supply the software to accredit up to 70,000 athletes, volunteers and officials, and run the Glasgow 2014 website.
Sturgeon is also the Scottish Government's leading voice on welfare issues – last week she announced an expert group to help devise a welfare system reflecting "Scottish values" and fairness under independence instead of the cuts being imposed by Westminster.
Protesters say Atos could not be further from those Scottish values, given its central role in the UK government's welfare reforms.
Atos Healthcare has a £110 million annual contract with the Department of Work and Pensions to run work capability assessments of the sick and disabled, and a £400m deal to assess mobility benefits.
Critics say the tests are flawed, degrading and inefficient, with one in six passed as fit to work winning an appeal against the decision.
The Atos sponsorship of the London 2012 Olympics and Paralympics led to protests, and similar actions are now planned in Glasgow. The 2014 HQ was occupied last month, and protesters have threatened to disrupt the Scottish equivalent of the Olympic torch relay if Atos is still a sponsor.
The SNP Government is funding about 80% of the £550m price tag for the Games.
However, a video of Friday's protest shows Sturgeon denying any say over the sponsorship: "Obviously the benefits side of this is not a matter for the Scottish Government, it's a UK Government issue ... I will take on board what you said to the Commonwealth Games. Obviously, it's not my decision in terms of sponsors."
Protester David Churchley, co-founder of the Black Triangle disability rights group, said Atos sponsorship was "absolutely scandalous and beyond belief" and that Sturgeon had tried to give protesters the brush off.
He said: "They have learned nothing from the Olympics. They're just riding roughshod over disabled people and those who support us. But Friday will be just one of many stunts we will be mounting up to the Games."
Sean Clerkin of Citizens United said: "The SNP Government is being hypocritical. They criticise the Tory-led Coalition for what they're doing to welfare, while welcoming Atos as sponsors of the Commonwealth Games.
"Nicola Sturgeon is the person talking about a welfare system with Scottish values. If she's going to live up to those values, she should ensure Atos is dropped as a sponsor."
An Atos spokesman said: "While we fully respect people's right to peaceful protest and understand this is a highly emotive issue, Atos is proud to be an official supporter of the Glasgow 2014 organising committee."
An SNP spokeswoman added: "We are opposed to the criteria and tests set by the UK Government that Atos deliver, and have made clear that they should reconsider this approach.
"We are looking forward to a positive Commonwealth Games that will be a great opportunity to showcase Scotland to the world."
The video of the protest can be seen at citystrolls.com.