Her predecessor, Hector Sants, became chief executive in July last year leaving the role free for Dewar - currently the FSA's director of markets - to step in.
She will also join the FSA Board as will be announced by HM Treasury.
In her new role, Dewar will have responsibility for all regulated markets and the related infrastructure such as clearing and settlements; the operation of the UK Listing rules; and regulation of firms or groups which conduct primarily wholesale or institutional business between professionals.
She has worked with the FSA since 2002 where she started out as head of primary markets in the markets division, before being promoted to director of markets in October 2005. She previously worked at the London Stock Exchange's Listing Authority after nearly 6 years at KPMG.
Hector Sants, FSA chief executive officer, said: "I am delighted that Sally will be taking on the role of wholesale managing director, which follows an extensive search both internally and externally to find the right person for this senior FSA position. Sally brings a hugely valuable mix of regulatory and commercial experience.
"In addition to her technical knowledge and strengths she is also widely recognised across the FSA as an outstanding leader. I have worked closely with Sally since I began at the FSA and I look forward to working with her in her new role."
In addition to this appointment, the FSA also announced that Thomas Huertas, current director of wholesale firms, will take on an enhanced role as banking sector leader, reporting directly to Hector Sants.
This has specifically been created to enable the FSA to ensure it has the necessary focus and resources to deliver the Tripartite authorities' initiatives to improve regulatory architecture of the banking industry.
Stephen Bland, currently director of small firms, will take Thomas Huertas's vacated role as director of wholesale firms. He will continue to lead the work on the Retail Distribution Review (RDR) for the immediate future.
Two other moves have been announced as part of the FSA's restructure to create a business unit that focuses on providing operational services to the FSA under a chief operating officer, David Kenmir, whilst bringing other aspects of regulation under the retail markets business unit.
Lesley Titcomb, currently director of regulatory transactions division, will become director of the expanded small firms and contact division.
Graeme Ashley-Fenn, currently director of the contact, revenue and information management division, will take responsibility for the new regulatory transactions and reporting division.
Both directors will now report to retail managing director Clive Briault. This change effectively turns three FSA divisions into two and generates cost savings and service improvements.
Hector Sants said that the reorganisation both underpinned and supported the FSA's determination to enhance its delivery to small firms.
All but Dewar will take up their new positions as of 1 February.
