Ma Ying-jeou, president of self-ruled, democratic Taiwan, where anti-Beijing sentiment has been rising ahead of elections, called for mutual respect for each other's systems and said Taiwan people were concerned about mainland missiles pointing their way.
The talks, at a luxury hotel in the neutral venue of Singapore, lasted less than an hour but were heavy with symbolism.
The two leaders shook hands and smiled in front of a mass of journalists when they met, with Xi wearing a red tie, the color of the Communist Party, and Ma a blue one, the color of his Nationalist Party.
Moving into a meeting room, Xi, speaking first and sitting opposite Ma, said Chinese people on the two sides of the Taiwan Strait had the ability and wisdom to solve their own problems.
"No force can pull us apart because we are brothers who are still connected by our flesh even if our bones are broken, we are a family in which blood is thicker than water," Xi said.
In response, Ma said he was determined to promote peace across the Taiwan Strait and that relations should be based on sincerity, wisdom and patience.
Ma also asked Xi indirectly to respect Taiwan's democracy.
"Both sides should respect each other's values and way of life to ensure mutual benefit and a win-win situation across the straits," he said.
The U.S. State Department said the meeting was part of an "historic improvement" in relations between Taiwan and China and called for further progress "toward building ties, reducing tensions and promoting stability."
China's Nationalists, also known as the Kuomintang (KMT), retreated to Taiwan after losing the civil war to the Communists, who are still in charge in Beijing.
The mainland has never renounced the use of force to bring what it considers a breakaway province under its control.
Speaking to reporters after the talks, Ma said he hoped Xi could pay attention to China's missile deployment - the island has long fretted about batteries pointed its way - to which Xi replied that was not an issue about Taiwan, he said.
"I at least raised the issue, and told him that the Taiwanese people have questions and concerns about it, and hope he will treat it with importance," Ma said.
Zhang Zhijun, the head of China's Taiwan Affairs Office, said Xi told Ma that the biggest threat to the peaceful development of relations was pro-independence forces.
"The compatriots on both sides should unite and firmly oppose it," Zhang said.
The meeting comes ahead of presidential and parliamentary elections on Taiwan which the independence-leaning Democratic Progressive Party (DPP) is favored to win, something Beijing is desperate to avoid.
Speaking in Taiwan, DPP leader and presidential candidate Tsai Ing-wen said she was disappointed Ma made no direct mention of Taiwan's freedom and democracy.
"We had expected President Ma to talk about Taiwan's democracy, freedom and the existence of the Republic of China," she said, in comments carried on Taiwan television stations, referring to Taiwan's official name.
"More importantly, the Taiwan people's right to choose freely. But he did not say a word of that."
While bilateral trade, investment and tourism have blossomed - particularly since Ma and his KMT took power in 2008 - there is deep suspicion on both sides and no progress has been made on any sort of political settlement.
No agreements had been expected in what was seen as a highly symbolic get-together in Singapore, a largely ethnic Chinese city-state that has maintained good ties with both for decades.
Protocol problems loomed large for democratic Taiwan and autocratic China and the two addressed each other as "mister" to avoid using the word "president", as neither officially recognizes the other as head of state.
Further underscoring China's sensitivities, state television only showed Xi's comments live, cutting away when Ma began to speak, prompting a flurry of complaints on Chinese social media about censorship. It later showed a recording of Ma's opening remarks.
Taiwan protests
The meeting comes as Xi hopes to cement his place among China's pantheon of great leaders and Ma, stepping down next year due to term limits, tries to shape his legacy marred by growing anti-Beijing feeling in Taiwan.
While China is laudatory, concerns have been raised in Taiwan, and on Saturday a few hundred people took to the streets in Taipei to protest against the meeting.
"Though he said he won't sign any agreements there, the Ma-Xi meeting itself shows there will definitely be some discussions or negotiations which have not been approved of by Taiwan's people," said protester Sung Yun-chuan.
Ma and Xi were due to have dinner together before flying out of Singapore separately.
Ma was due to present Xi bottles of spirits made on two groups of islands just off the mainland that have been occupied by Taiwan forces since the end of the civil war.
He would also present Xi with a ceramic sculpture of a Taiwan blue magpie perched on a leafy green branch as a gift for their first meeting, a bird unique to the island, Taiwan's presidential office said.
