Houghton, who ran the Microsoft Australia operation for three years, has been promoted to take the position of vice-president for the US South Region.
Vamos becomes the first Australian managing director of the local Microsoft operation since 1997.
"It's a pretty natural transition for me," Vamos said. "I have worked very well with Microsoft and I have worked very closely with Paul Houghton."
"I've been in the tech industry for many years, and Microsoft is a great company working in a broad range of technology areas that I'm interested in," he said.
No replacement for Vamos at ninemsn has yet been decided on, he said, although the company's board had already begun the process of selection.
Vamos said he had not been given any specific agenda for Microsoft, beyond maintaining the company's ongoing success in this country.
"Australia is one of Microsoft's strongest operations," Vamos said, pointing to the strength of the local Microsoft team management team.
Vamos is uniquely positioned to take the role, having worked closely with Microsoft, the Packer family's PBL, and Packer's listed online vehicle ecorp, since joining ninemsn as managing director in 1997.
Prior to ninemsn, Vamos had been managing director of Apple Australia.
Under Houghton's leadership, Microsoft Australia has grown. In particular, Houghton built a strong industry leadership profile for Microsoft within Australia, particularly among governments and key policy makers.
"Australia is an important market for Microsoft, I have a terrific team and I'm proud of our accomplishments and the progress we have made to grow the business in a period of tremendous change and uncertainty," Houghton said.
Vamos takes the reins at Microsoft Australia on February 1.