The welcome came as the authoritarian leader is being criticised in the West for a bloody crackdown on protesters.
President Islam Karimov is "an old friend of the Chinese people," Chinese President Hu Jintao said during a meeting at the Great Hall of the People, the seat of China's legislature.
"For a long time, you've made efforts towards friendship with China. For this, we express high praise," Hu told Karimov.
The Uzbek leader responded by saying that "China is of course one of the world's most important countries. We see this visit as the most new important stage in bilateral relations".
The warm welcome highlights China's focus on strategic stability in the former Soviet states of Central Asia, a region that Beijing considers a hotbed of Islamic activism that could spread to its own territory.
Red carpet ceremony
Beijing also is keen to find partners in its campaign against Muslim activists - even at the cost of playing down international concerns about the Uzbek government's use of force.
State television showed the two leaders smiling and shaking hands.
Earlier, Chinese officials greeted Karimov at the Beijing airport in a red-carpet ceremony with flower bouquets.
"This is a good opportunity for President Karimov. He's facing international pressure, but in China or Russia,
he will get the support
Taiwan's National Chengchi University
"The peace and stability of the area is important to the environment of the border areas in China," Zhan Yao, a Central Asia specialist at the Shanghai Institute of Foreign Studies, said
The 13 May protests in the eastern city of Andijan were triggered by the prosecution of businessmen charged with being sympathisers of "Islamic extremists". Troops moved in and shooting broke out.
Uzbek opposition groups and human-rights activists claim more than 700 people - mostly unarmed civilians - were killed.
If true, that would make it one of the deadliest crackdowns on protesters since the massacre of demonstrators in China's Tiananmen Square in 1989.
Karimov's government put the death toll at 169 and said most were insurgents.
Karimov has resisted calls by Nato and the European Union for an independent investigation of the events.
Up to 700 people are thought to
have been killed in Andijan
The US also has criticised the crackdown and said it hopes for more democracy in Uzbekistan.
But China and Russia have been more supportive. The unrest occurred about 190km from China's western region of Xinjiang, which shares Uzbekistan's Muslim religion and Turkic language roots.
Chinese authorities claim Uighur separatists in the area are fighting for an independent theocratic state and are part of an international "Islamic terrorist network".
Chinese Foreign Ministry spokesman Kong Quan said on Tuesday that China's leaders "firmly support the efforts by the authorities of Uzbekistan to strike down the three forces of terrorism, separatism and extremism".
While the three-day visit was a courtesy trip scheduled after Hu went to Tashkent last year, it gave Karimov a way to underline that China is on his side.
"This is a good opportunity for President Karimov," Joshua Lung, an assistant research fellow at the Institute of International Relations in Taiwan's National Chengchi University, said.
"He's facing international pressure, but in China or Russia he will get the support he needs."