The two leaders hailed their strategic ties in defiance of the West.
Thursday's visit was Ms von der Leyen's third to Ukraine since Russia invaded in February, but this was different.
"We will never be able to match the sacrifice that the Ukrainians are making," she said alongside Ukrainian President Volodymyr Zelenskyy.
"But what we can tell you is that you'll have your European friends by your side as long as it takes."
Ms von der Leyen also said that she wanted Mr Putin to face the International Criminal Court over war crimes in Ukraine.
"That Putin must lose this war and must face up to his actions, that is important to me," she told the TV channel of German news outlet Bild.
On her arrival in Ukraine, Ms von der Leyen said her talks with the country's leaders would be about "getting our economies and people closer."
Ukraine war latest - in pictures
Kyiv gained EU candidacy status in June at the same time as former Soviet state Moldova, which shares a border with Ukraine.
Like its neighbour, Moldova has had Russian troops stationed in an eastern breakaway region.
Mr Zelenskyy said his country wanted to join the European single market before a decision was made on whether to grant Kyiv full EU membership.
The historic candidacy vote angered Moscow, which has tried to retain political and military influence in Ukraine and Moldova since the collapse of the Soviet Union three decades ago.
Zaporizhzhia latest - in pictures
EU countries have staunchly supported Ukraine since Moscow invaded by imposing economic penalties on Russia.
Many members of the bloc have supplied Kyiv with advanced weapons that have helped Ukrainian forces in recent weeks to recapture large areas of territory.
Germany's Defence Minister, Christine Lambrecht, on Thursday pledged more weapons, saying Berlin will provide armoured vehicles and rocket-launch systems but not the battle tanks sought by Ukraine.
Ms von der Leyen said just before her trip that the waves of EU sanctions against Russia would remain and that Europeans must keep their resolve against Moscow.
"I want to make it very clear, the sanctions are here to stay," she told the European Parliament.
IAEA issues warning over military activity near Zaporizhzhia nuclear plant - video
The Kremlin maintains that Russia has weathered the economic penalties and Moscow has responded by reducing or halting entirely gas flows to European countries.
With winter fast approaching, this has forced the EU to find alternative supplies, agree on plans to cut consumption and introduce financial support amid soaring prices.
Ukrainian energy plants including Zaporizhzhia, Europe's biggest nuclear plant, have been hit by Russian strikes.
The UN nuclear agency on Thursday asked Russia to withdraw its troops from Zaporizhzhia, diplomats said.
Ukraine's forces have posted slow but steady gains in the southern Kherson region near the Black Sea.
The Ukrainian presidency said on Thursday that intense fighting was continuing around that southern front, and that the military situation "remains extremely difficult."
Local officials in the region around Mr Zelenskyy's hometown of Kryvyi Rih reported more Russian strikes on Thursday after attacks damaged a dam and left dozens of homes flooded.
Zaporizhzhia nuclear power plant attacked - in pictures
In the eastern Donetsk region, which has been partly controlled by Russian-backed separatists since 2014, shelling killed two civilians and wounded 13.
In the Ukrainian-held Donetsk town of Bakhmut, streets were deserted and the nearby artillery could be heard in the town's centre, AFP reported.
A residential building hit by Russian strikes overnight was still on fire, with thick smoke rising as firefighters battled the blaze.
At the meeting in Uzbekistan, Mr Putin criticised attempts to create a "unipolar world" and praised China's stance on the conflict.
"We highly appreciate the balanced position of our Chinese friends in connection with the Ukrainian crisis," Mr Putin told Mr Xi.