The meeting brought Washington and Beijing into contact a day after Li warned major powers must manage differences to avoid a "new Cold War", and ahead of the G20 summit in New Delhi this week that Chinese President Xi Jinping will miss.
Interactions between the officials from the world's top two economies are being closely watched as they seek to control tensions that risk flaring anew over issues ranging from Taiwan to ties with Moscow and the competition for influence in the Pacific.
"Every leader has an equal responsibility to not create new conflicts, to not create new tensions, and at the same time we also have a responsibility to lower heated tensions," Indonesian President Joko Widodo, chair of the Association of Southeast Asian Nations (ASEAN), said in closing remarks.
"I can guarantee you that if we are not able to manage differences, we will be destroyed."
Harris spoke about "Russia's illegal invasion of Ukraine", maritime challenges in the South and East China Seas and the growing threat of North Korean missile programmes, Daniel Kritenbrink, US assistant secretary for East Asia and Pacific affairs, told a briefing.
But a leaders' statement seen by AFP omitted any mention of the waterway or the Ukraine war.
A Southeast Asian diplomat, who declined to be identified, told AFP a draft paragraph in the leaders' statement referring to the South China Sea was rejected.
"China objects of course and this is a negotiated text. This is also why there is no Ukraine paragraph because Russia objects," the diplomat said.
Thursday's 18-nation summit was the first time top US and Russian officials have sat around the same table in almost two months, after US and European officials condemned Lavrov at a July ministerial meeting over Russia's invasion of Ukraine.
Lavrov spoke of the risks of the "militarisation of East Asia", accusing the NATO alliance of moving into the region, Russia's foreign ministry said in a statement Thursday.
A chair statement released by Indonesia said each country "reiterated our national positions" on the Ukraine war in the meeting and "reaffirmed our shared commitment to safeguarding and promoting peace, security and stability in the South China Sea".
- 'Unacceptable' -
Indian Prime Minister Narendra Modi, Japanese leader Fumio Kishida, South Korean President Yoon Suk Yeol, Canada's Justin Trudeau and Australian premier Anthony Albanese all attended the summit, as well as ASEAN leaders.
Albanese met Li on the sidelines of the summit, confirming he would visit China later this year as Canberra seeks to stabilise ties with Beijing.
China's premier in turn said Beijing was ready to resume bilateral exchanges after years of friction, state news agency Xinhua reported.
G20 host Modi told ASEAN leaders on Thursday morning it was essential to make collective efforts to ensure a "free and open Indo-Pacific", using another term for the Asia-Pacific region.
Yoon told officials any attempts to change the status quo in the South China Sea were "unacceptable" and called for a "rules-based maritime order", according to his office.
Philippine President Ferdinand Marcos Jr said regional powers must oppose the "dangerous use of coast guard and maritime militia vessels" in the disputed waterway, according to his speech released by the presidential palace.
- 'Systematic repression' -
While the gathering can bring major players together, its ability to help resolve a range of regional and global disputes is limited, experts say.
"It has been turned into a forum for talking points," said Aaron Connelly, senior fellow at Singapore-based think tank IISS.
Thursday's meeting was more geopolitical in scope but big powers used earlier talks in Jakarta to shore up alliances and lobby the Southeast Asian bloc.
Li travelled on a Chinese-funded high-speed train project between the capital Jakarta and the Javan city of Bandung with a senior Indonesian minister on Wednesday.
Harris held separate meetings with Widodo and Marcos -- whose countries are both ASEAN members -- on the sidelines of the summit.
The ASEAN summit this week was dominated by the Myanmar crisis, where leaders called on the country's junta rulers to stop attacks on civilians.
United Nations Secretary-General Antonio Guterres said before he met ASEAN leaders on Thursday that hopes of a return to democracy in Myanmar were being squashed.
"Brutal violence, worsening poverty, and systematic repression are crushing hopes for a return to democracy," Guterres said.
Myanmar is also an ASEAN member but its junta leaders are banned from high-level bloc meetings.
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