Ties between the two neighbours -- both of them US allies threatened by nuclear-armed North Korea -- remain tense over statues placed outside Japanese diplomatic missions by South Korean activists in memory of the victims.
Last month South Korean President Moon Jae-In slammed the agreement as "seriously flawed" and told officials to re-examine it.
But now Seoul's foreign minister Kang Kyung-wha has said it was an "undeniable fact" that both governments had formally endorsed it.
"Considering that, our government will not demand renegotiation of the deal to the Japanese government," Kang told reporters Tuesday.
But Seoul will not use any more of Tokyo's money for the survivors, replacing the funds from its own budget, Kang said, urging Tokyo to offer a "voluntary and sincere apology".
The financial move seeks to take the moral high ground and avoid perceptions that Tokyo has settled the issue by way of reparations.
Japan has urged South Korea to stick with the 2015 deal, saying any attempt by Seoul to revise it "cannot be acceptable whatsoever" and would leave bilateral ties "unmanageable".
It is the second time the left-leaning Moon's government has avoided implementing a campaign promise made to appeal to his base on practical grounds -- a pledge to phase out nuclear power in the resource-poor South was outsourced to a "citizen jury", which decided that the country needed atomic energy.
Mainstream historians say as many as 200,000 women - mostly from Korea but also other parts of Asia including China - were forced to become sex slaves for Japanese soldiers during the war.
The Japanese government denies it is directly responsible, insisting that "comfort women" were recruited by civilians and that the army brothels were commercially operated.