"Putin is my best friend and a good colleague", Xi said in comments published on the Kremlin's website.
The pandas, who could be seen chomping bamboo as Xi and Putin arrived, will living in a specially built enclosure.
The visit comes five years after Moscow's annexation of Crimea in 2014 led to a serious rift with its Western partners and subsequent turn toward its neighbour to the east.
Ahead of their closed-door meeting in the Russian capital Wednesday, Putin said relations between the erstwhile Cold War foes had "without any exaggeration, reached an unprecedented level".
Speaking about economic cooperation, Putin noted the increase in trade and the fact that Russian-Chinese cooperation in the energy sector had become strategic in nature.
Two-way trade between China and Russian Federation hit a record high of over $100 billion past year.
A special exhibition opened on Wednesday in the Bolshoi Theater, where a ceremonial event dedicated to the anniversary of the establishment of diplomatic relations will be held with the attendance of the two leaders. They pledged to develop a comprehensive partnership and boost coordination on security issues.
"We highly appreciate that friendly gesture", Putin said with a smile.
Bodies of five missing mountaineers spotted on Nanda Devi
Local media reports say the group were attempting to reach the summit of India's second-highest peak Nanda Devi in Uttarakhand. An Australian climber, who is now recovering in a Nepalese hospital, was rescued after he collapsed while climbing Everest.
Xi will also attend the 23rd St. Petersburg International Economic Forum and address its plenary session during the visit. The share of trade with Russian Federation held by China has nearly doubled to 20% since then, at Europe's expense.
'The pivot really is happening, ' he said.
In 2018, Chinese tourists made 1.8 million trips to Russia while Russian travelers made almost 2 million trips to China.
"Despite all the difficulties, China became a significant creditor and rather significant investor" in Russian Federation at a time when many other investors preferred to pack their bags.
Wu Hongwei, a researcher of China-Russia relations at the Chinese Academy of Social Sciences, said the two countries share the same position on building a more stable and multipolar world, and they have sent such signals through supporting and coordinating with each other on global occasions.
Both countries underlined their commitment to maintain good relations with Iran.
For China, a trade war with Washington continues to rage, and neither President Trump's administration nor Beijing is showing any signs of letting up.
Putin and Xi were meeting in Moscow as world leaders gathered on the south coast of England to mark the 75th anniversary of the D-Day landings.
After Washington criticised its rights record, Beijing issued a travel warning to Chinese nationals Tuesday about crime and police harassment in the United States.