Cummins, who has struggled with a number of injuries since his sole test against South Africa in 2011, had suffered a stress fracture in his lower back, scans revealed.
"Consequently Pat will be unable to participate in the Bangladesh test series and will now enter into a lengthy rehabilitation program," team physiotherapist David Beakley said in a statement on Thursday.
Fast-bowling all-rounder James Faulkner will replace Cummins in the squad for the tests in Chittagong and Dhaka next month, Cricket Australia said.
The latest breakdown will be a bitter pill for the 22-year-old Cummins, who has suffered two previous back stress fractures, along with a serious heel injury and a side strain since his dazzling seven-wicket haul as an 18-year-old debutant in Johannesburg.
He had been on the verge of a test recall after featuring in 13 one-day internationals and four Twenty20 matches over the past year, a rare injury-free period.
"This is really unfortunate for Pat and I know how disappointed he will be," selectors chairman Rod Marsh said.
"He is a young bowler with a bright future for Australia and we were really pleased with how he bowled in the UK."
Cummins joins David Warner on the sidelines, the opening batsman ruled out of Bangladesh weeks ago after breaking a thumb during the ODI series in England.
Faulkner is back in the frame two years after his first and only test against England, a dead rubber in the 2013 Ashes at The Oval in which he took six wickets.
Man-of-the-match in Australia's victorious World Cup final against New Zealand in March, the 25-year-old will be eager to re-ignite his international career after being booted out of the one-day team in July for being caught drink-driving in England.
"James comes back into the Australia test side having only played the one test, but he is an exciting young bowler who could be very handy in the conditions we are likely to see in Bangladesh," Marsh said.
Faulkner is likely to be second in the queue behind fast-bowling all-rounder Mitchell Marsh, however, who is in the 15-man squad along with seamers Peter Siddle, Mitchell Starc and the uncapped Andrew Fekete.
(Reporting by Ian Ransom; Editing by Sudipto Ganguly/Amlan Chakraborty)
