The Crows will pay $11.326 million while the Power will pay $6,985 million over the next 15 years.
SANFL chairman John Olsen said Thursday's signing of documents - that handed the licences back to the clubs - was the most significant day for SA football since Adelaide's inception to the AFL in 1991.
Both clubs now answer to the AFL Commission, not the SANFL.
"This is quite a monumental occasion,” said Adelaide chairman Rob Chapman. “Independence is the natural evolution for our club.
“That said we will continue to work closely with all parties to ensure the best interests of South Australian football are at the forefront of everyone’s thinking.
“We were formed by, and have lived under the control of the SANFL for 23 years.
“Effective today we stand on our own two feet and will operate independently.”
Olsen said the two AFL licences had proved a "great investment for football" in South Australia.
“The licences have generated in excess of $180 million in stadium income and sub-licence fees since 1991," he said.
"Of that,the SANFL has spent in excess of $30 million on junior development programs, $11 million on our talent programs, $19 million on the development of umpires for the code and another $19 million on the marketing of the sport itself.
"We have also passed a further $88 million to the SANFL clubs."
Twitter: @AFL_Harry