Politics at play?
For China, the FTA represents a "political success" as it becomes more assertive about territorial rights and seeks to balance U.S. influence in Asia.
"China has scored a political success against Japan by concluding an FTA that freezes out Japan from trade liberalization in Northeast Asia," said Rajiv Biswas, Asia-Pacific chief economist at IHS.
"Particularly, since plans for a trilateral FTA between China, South Korea and Japan have been stalled since 2012. The impasse over the planned trilateral FTA reflects the escalation in bilateral political tensions between China and Japan since 2012 over disputed territorial claims," he added.
Apart from rival claims in the East China Sea with long-time rival Japan, China China is also engaged in a territorial dispute in the South China Sea with Vietnam, the Philippines, Taiwan, Malaysia and Brunei.
South Korea is the only country in the region with which China doesn't have a maritime dispute. Both countries have seen warmer ties as of late, with China's Xi visiting Seoul in July.
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"I think China chose to build a long-term relationship with South Korea by penetrating economic issue first. Korea and the U.S. have been strengthening security-ties these days but at the same time, Korea leans toward China economically," said Yooil Bae, assistant professor of Political Science, School of Social Sciences, Singapore Management University.
As Washington considers installing an advanced missile defense system in South Korea, the FTA will strengthen China's voice on that issue, Bae said. "It will make competition between the two super powers more complicated."