The US president also raised concerns about the arrest of opposition figure Alexei Navalny and Russia’s involvement in a major cyber espionage campaign and bounties on American troops in Afghanistan, US officials said.
In his call with Mr Putin, the US leader declared that he knew that Russia attempted to interfere with both the 2016 and 2020 elections.
On Monday, he told reporters he hoped the US and Russia could co-operate in areas where both see benefit.
“I find that we can both operate in the mutual self-interest of our countries as a New Start agreement and make it clear to Russia that we are very concerned about their behaviour, whether it’s Navalny, whether it’s SolarWinds or reports of bounties on heads of Americans in Afghanistan,” Mr Biden said.
Moscow reached out last week to request the call, according to the US officials.
Mr Biden agreed but wanted first to prepare with his staff and speak to European allies, including the leaders of Britain, France and Germany.
The US president told Mr Putin that his administration is assessing the SolarWinds breach and the reports that Russia offered the Taliban bounties to kill American troops in Afghanistan.
He added that the US is willing to defend itself and will take action, which could include further sanctions, to ensure that Moscow does not act with impunity, according to the administration officials.
“President Biden made clear that the United States will act firmly in defence of its national interests in response to actions by Russia that harm us or our allies,” said the White House in a statement about the call.
“The two presidents agreed to maintain transparent and consistent communication going forward.”
The Kremlin’s readout did not address the most contentious issues between the countries, though it said the leaders also discussed other “acute issues on the bilateral and international agenda”.
It described the talk as “frank and businesslike” - often a diplomatic way of referring to tense discussions.
It also said Mr Putin congratulated Mr Biden on becoming president and “noted that normalisation of ties between Russia and the US would serve the interests of both countries”.
Among the issues it said were discussed were the coronavirus pandemic, the Iran nuclear agreement, Ukraine and issues related to trade and the economy.
The two presidents agreed to have their teams work urgently to complete an extension of New Start, the last remaining US-Russian arms control treaty, before it expires next month.
“In the nearest days, the parties will complete the necessary procedures that will ensure further functioning” of the pact, the Kremlin said in its readout of the call.
The call came as Mr Putin considers the aftermath of pro-Navalny protests that took place in more than 100 Russian cities over the weekend.
Mr Biden’s team has already reacted strongly to the crackdown on the protests, in which more than 3,700 people were arrested across Russia, including more than 1,400 in Moscow. More protests are planned for the coming weekend.
Mr Navalny, an anti-corruption campaigner and Mr Putin’s best-known critic, was arrested on January 17 as he returned to Russia from Germany, where he had spent nearly five months recovering from nerve agent poisoning that he blames on the Kremlin. Russian authorities deny the accusations.
Mr Biden has previously condemned the use of chemical weapons.
Additional reporting by Associated Press.