The announcement follows a lengthy delay that had caused anger on Capitol Hill and raised questions about Trump's willingness to confront Moscow.
The measures target five entities and 19 individuals, including the FSB, Russia's top spy service; the military intelligence agency, or GRU; and 13 people recently indicted by Robert Mueller, the US special counsel handling a sprawling Russia probe.
Sanctions were also levied against individuals behind the separate Petya cyberattack and an "ongoing" attempt to hack the US energy grid.
The move comes despite Trump's repeated denial that Russia tried to tilt the election in his favour, fearing it could call his victory over Hillary Clinton into question.
News that makes sense
Your trusted source for staying up-to-date with the world around you. Get free daily news updates and analysis, straight to your inbox.
The president has also decried more damaging allegations that his campaign colluded with the Kremlin -- the subject of Mueller's ongoing investigation that has seen several key aides indicted or make plea deals.
"It took 14 months," leading Democratic Senator Amy Klobuchar said of the sanctions. "Finally."
"Now we must protect our elections going forward," she added.
Treasury Secretary Steven Mnuchin said the decision showed the administration was "confronting and countering malign Russian cyber activity, including their attempted interference in US elections, destructive cyberattacks, and intrusions targeting critical infrastructure."
"These targeted sanctions are a part of a broader effort to address the ongoing nefarious attacks emanating from Russia," he added.
Moscow's 'response'
Moscow said it was preparing its response.
"We view this calmly. We have begun to prepare response measures," deputy foreign minister Sergei Ryabkov told Interfax news agency.
He claimed the US move was designed to coincide with Russia's presidential election on Sunday.
Many of the main entities and individuals hit -- including the spy agencies and 'troll factory' boss Yevgeny Prigozhin -- already face assets freezes and travel bans, either put in place under Barack Obama's administration or for actions linked to Russia's actions in Ukraine.
But the decision heaps pressure on Moscow as it faces separate punitive measures for an alleged attempt to kill a Russian-born British informant with a nerve agent west of London.
Britain, France, Germany and the United States condemned the attack on the Russian ex-spy and his daughter, saying there was "no plausible alternative explanation" to Moscow's involvement.
Trump said Thursday "it looks like" Russia was behind that attack.
"I've spoken with the (British) prime minister and we are in discussions," he added. "A very sad situation. It certainly looks like the Russians were behind it. Something that should never, ever happen, and we're taking it very seriously."
Moscow has denied being involved, claiming the British government was trying to "deflect attention" from difficult negotiations with the European Union over Brexit.
