In a carefully worded statement, Toomey noted that Trump "has the legal and constitutional authority to grant clemency for federal crimes," arguing that this power "should be used judiciously and very rarely by any president."
The Republican described former special counsel Robert Mueller's investigation into Russian election interference as "badly flawed" but expressed opposition to Trump's decision to pardon Stone.
"While I understand the frustration with the badly flawed Russia-collusion investigation, in my view, commuting Roger Stone's sentence is a mistake."The senator added that the longtime GOP operative was "duly convicted of lying to Congress, witness tampering, and obstructing a congressional investigation conducted by a Republican-led committee."
Toomey pointed out that Attorney General William Barr -- who allegedly advised Trump against intervening in the case -- recently described Stone's sentence as "fair."
"Any objections to Mr. Stone's conviction and trial should be resolved through the appeals process," the Pennsylvania Republican concluded.
Stone, a longtime ally of Trump, was convicted of obstruction of justice and witness tampering. The Republican operative was also found guilty of lying to the United States Congress during its investigations into Russian interference in the 2016 presidential election.
Trump and his Republican allies have long dismissed investigations into the Kremlin's election meddling as a "hoax" meant to derail his presidency. Mueller and his investigators found that Moscow intervened in the 2016 election to help Trump win, but failed to prove that members of the president's campaign conspired with the Russian government.
Toomey is the second Republican senator to criticize Trump's decision.
Romney has repeatedly clashed with Trump. Notably, he was the only Republican to vote for the president's conviction in the United States Senate's impeachment trial.
In a tweet published on Saturday, Trump defended his decision, writing that Stone "was targeted by an illegal Witch Hunt that never should have taken place."
As NPR noted, some Republicans have remained silent, while others openly supported the president's decision. Notably, Sen. Lindsey Graham of South Carolina and Rep. Jim Jordan of Ohio commended the president for intervening in the case.
Trump commuted Stone's sentence on Friday, drawing the ire of Democratic politicians. Some of the president's advisers were reportedly opposed to the idea, but those who lobbied on Stone's behalf prevailed.