The cricket body confirmed in a statement on Thursday that Saker would leave the post after a home season in which Australia's fast bowlers were criticized for going six test matches without an lbw decision against India and Sri Lanka.
Head coach Justin Langer said he reached a mutual agreement with Saker, a former England bowling coach, that it was time for the pair to part ways.
"David and I have had ongoing discussions over the past nine months about his role with the team, and we agreed it's the right time to head in a different direction in the best interests of the team," Langer said in the statement.
Troy Cooley will serve as acting bowing coach on upcoming limited-overs tours of India and against Pakistan in the United Arab Emirates.
Langer is likely to hire a new bowling coach ahead of the team's marathon tour of England, during which Australia will defend both the World Cup and Ashes series.