The executive abruptly left the software giant following the release of Windows 8, with former Microsoft engineer Hal Berenson since insinuating in a blog post that he attempted a takeover of the mobile OS.
"I never initiated any discussions to bring together the organisations/products you describe," Sinofsky wrote in response to the posting. "No one [outside the Windows division] ever approached me to manage them as part of Windows 7 or 8."
No official reason for Sinofsky's departure was given, but reports suggest company CEO Steve Ballmer had him step down because he was "divisive" among the firm's other executives.
However, Ballmer paid tribute to the ex-Windows head upon his resignation. "I am grateful for the many years of work that Steven has contributed to the company," he said. "The products and services we have delivered to the market in the past few months mark the launch of a new era at Microsoft."
Microsoft released its Windows 8 operating system for PCs and tablets to generally positive reviews last month.