In a joint press conference, Putin said that the leaders touched on issues including tensions on the Korean peninsula and the situation in Syria during their first summit.
"I consider them (the talks) very successful and useful," Putin said, praising the "frank and business-like atmosphere" of the summit.
He said Trump had raised accusations of Russian interference in US elections.
Trump had winked at Putin as he met him at the summit.
"I had to repeat what I have already said many times before - the Russian state has never interfered and is not planning to interfere in the USA's internal affairs," Putin said.
"It is obvious to everyone that bilateral ties are going through a difficult period. However, there are no objective reasons for these difficulties, the current tense atmosphere," he said.
Putin, basking in congratulations from Trump and other world leaders for the successful staging of the World Cup in Russia, said: "The time has come to talk in a substantive way about our relations and problem areas of the world."
Trump added: "Frankly, we have not been getting along for the last number of years. And I really think the world wants to see us get along. We are the two great nuclear powers."
Sergei Lavrov, the Russian foreign minister, said separately that the talks were "better than super" in comments reported by Russian news agencies.
After a stormy NATO summit in Brussels last week, Trump was accused by critics of prioritising his ties to Putin over the transatlantic alliance.
Trump's morning remarks, however, were different.
"NATO's never been stronger. NATO has never been more together," he said at a breakfast meeting with the Finnish President Sauli Niinisto. US allies "are now agreeing to pay" their fair share, Trump added.
Trump's comments come after he demanded last week that NATO allies "reimburse" the US for defence costs.
European Union President Donald Tusk, hit back against comments and said Trump was guilty of "spreading fake news" with his remark about foes.
He warned that the trade tensions could spiral into violent "conflict and chaos".
"Europe and China, America and Russia, today in Beijing and in Helsinki, are jointly responsible for improving the world order, not for destroying it," he tweeted.
"I hope this message reaches Helsinki."
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