He called the alleged chemical attack in Douma a scripted play.
According to Syrian medics and a statement by the World Health Organisation, more than 40 people died in an April 7 strike on the former rebel outpost of Douma of symptoms consistent with the use of chemical weapons.
Earlier this week, a USA attack on Syria looked imminent as Trump warned Russian Federation to "get ready" for missiles, but then on Thursday he appeared to back away, tweeting that an American attack could come "very soon or not so soon at all".
"The goal of our actions tonight is to establish a strong deterrent against the production, spread and use of chemical weapons", Trump said.
Maj Gen Konashenkov said Britain was "directly involved in the provocation".
A senior French official noted that President Emmanuel Macron did not tell Putin about the strikes when they spoke on the phone Friday, but "certain de-confliction mechanisms" had already been triggered by that point, and "both knew that a new phase was going to begin quickly".
According to a statement by the French presidency, Mr Macron called for dialogue between France and Russian Federation to "continue and intensify" to bring peace and stability to Syria.
"With our allies, we ensured that the Russians were warned ahead of time", said French Defense Minister Florence Parly. Putin and Macron instructed their foreign and defense ministers to maintain close contact to "de-escalate the situation", the Kremlin said.
Fyodor Lukyanov, head of the Council for Foreign and Defense Policies, an association of top Russian foreign policy and security experts, said on state TV that Moscow's warning to strike back "clearly hasn't come unnoticed by the Pentagon, and the strike was quite careful".
The United States is preparing new sanctions on Russian Federation over its continued support of Syrian President Bashar-al Assad, the US ambassador to the United Nations, Nikki Haley, said Sunday.
Loud explosions early yesterday rocked the Syrian capital and filled the sky with heavy smoke after US President Donald Trump announced airstrikes in retaliation for the country's alleged use of chemical weapons.
The strikes have come after a week-long worldwide push to punish the Assad regime after images and videos emerged on April 7 suggesting civilians - including children - had suffered a chemical attack in Douma. "Russian Federation can complain all it wants about fake news, but no one is buying its lies and its cover-ups".
Trump then singled out Russian President Vladimir Putin and said, "Russia must decide if it will continue down this dark path or if it will join with civilized nations as a force for stability and peace".
"Why would the winning side use (chemical) weapons", he said in a video address at a Hezbollah campaign event for Lebanon's parliamentary elections in May.
A fact-finding mission from the Organization for the Prohibition of Chemical Weapons is expected to arrive in Douma on Saturday.
Nebenzia told the Security Council "before the investigation even occurred, guilty parties were identified". In a reference to the US, he said that "it would only benefit those who are protected by the ocean and expect to sit there and engage in continuous efforts to stir up the region in order to advance their geopolitical goals".
Russia's defence ministry said no Syrian civilians or military were killed in the attacks.