According to a statement, Chippendale is leaving to "pursue other opportunities".
He was promoted from deputy sales director in January 2003, following Peter Shea's decision to step down.
However, there has been speculation that Chippendale and Milligan, the former deputy chief executive of five, clashed. Milligan, who joined the Sky sales house, Sky Media, in the newly created position of managing director, is known for his hands-on approach.
A Sky spokesman said no decision on a replacement had been made, but Milligan could look to bring in some of his former sales team at five.
Chippendale represented Sky on the board of Barb and was its member on the new television marketing body. A spokesman said these responsibilities would now fall to Milligan until a decision on a replacement had been made.
Chippendale was instrumental in championing interactive advertising to clients and in the creation of Sky's 20,000-strong research panel which marries the viewing habits of satellite viewers with their purchasing behaviour.
In a statement, Dawn Airey, the managing director of Sky Networks, said: "Mark has made an enormous contribution to Sky's success and in particular to the sustained growth of its advertising operation. We thank him for all of his efforts and wish him well for the future."