The watchdog reviewed whether the integration of the telecommunications and telecom equipment-making businesses of SK Telecom with Hynix's semiconductor manufacturing would stifle market competition.
Although the two companies are both major players in the mobile and chip sectors, their technologies, supply channels and clients are different, the commission said.
"We concluded that SK Telecom's Hynix acquisition does not limit market competition," the Fair Trade Commission's Chairman Kim said in a statement.
SK Telecom controls 54.5 percent of South Korea's wireless market and Hynix supplies around 20 percent of the global dynamic random access memory (DRAM) market.
Last month, SK Telecom agreed to buy the 21.05 percent stake in Hynix for 3.43 trillion won (US$3.06 billion) from creditors.
The deal is expected to be finalized next month.
The acquisition is expected to help the mobile giant enter into the memory chip sector and compete with Samsung Electronics Co., the world's top memory chipmaker.