Abe and Trump also agreed that pressure on North Korea must be raised, Abe told reporters after the conversation.
Park Soo-hyun, the spokesman for Seoul's presidential office, said the leaders had reached an agreement in principle to loosen - "to the extent hoped by the South Korean side" - limits on the South's ballistic missile capability.
"It is believed that the U.S. is positive toward rotational deployment of F-22 and F-35B jets over Korea as it remains firm in countering North Korea's provocations", a government source said.
Trump, who has warned that the USA military is "locked and loaded" in case of further North Korean provocation, reacted angrily to the latest missile test, declaring on Twitter that "talking is not the answer" to resolving the crisis.
Meanwhile, the White House said in a statement, without explicitly mentioning the missile guidelines, that the leaders "agreed to strengthen" their alliance and Seoul's defense capabilities.
Trump also gave "conceptual" approval to the purchase by the South of billions of dollars of United States military hardware, the White House said. Another issue discussed by the defense chiefs was increasing the strength of the missiles in South Korea's arsenal.
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Trump says he will discuss South Korea trade deal with senior advisers
But he also noted the renegotiation was an opportunity to address those concerns. Lighthizer's office after the talks said the US still has concerns about KORUS.
Will Piyush Goyal put railways on track?
The saffron party has also been wooing Christians and his induction is likely to help this cause. Pradhan and Naqvi retained their portfolios of Oil and Gas and Minority Affairs respectively.
The missile guidelines that Seoul sought to revise was first stipulated in 1979 to contain a regional arms race.
In 2012, the revision allowed Seoul to increase the maximum allowable missile range to 800km from the previous limit of 300km.
Impoverished North Korea and the rich, democratic South are technically still at war because their 1950-53 conflict ended in a truce, not a peace treaty.
Still, the South Korean president continued to emphasize the importance of dialogue with its neighbor in the phone call with his American counterpart.
Trump has insisted that "all options" are on the table in an implied threat of pre-emptive military action, while on Thursday US heavy bombers and stealth jet fighters took part in a joint live fire drill in South Korea intended as a show of force.
The quake, if confirmed to be a nuke experiment, would be the latest in a recent series of the communist state's provocations, including its two tests of an intercontinental ballistic missile (ICBM) in July.