The new sanctions announced on Tuesday mark the first time the US has placed elected officials from the powerful Shia movement on its sanctions blacklist.
Lebanon "regrets" the US move, "especially in terms of targeting two elected deputies", Michel Aoun said in a statement.
The decision "contradicts previous American positions that confirm Lebanon's commitment to international conventions on combating money laundering and preventing its use in terrorist attacks", he added.
Aoun assumed the presidency in 2016 with the backing of Hizballah, allied since 2016 with his Maronite Christian party, the Free Patriotic Movement.
Prime Minister Saad Hariri, a prominent Sunni opponent of Hizballah, said the US had taken a "new course" by sanctioning lawmakers, but added it would "not affect" his government, which includes ministers from Hizballah.
"It is important that we preserve the banking sector and the Lebanese economy and this crisis will pass sooner or later," Hariri added.
Parliament speaker Nabih Berri, himself a Shia, condemned the sanctions against the officials of Hizballah, a sworn enemy of Israel and ally of Iran, as an "aggression" against Lebanon, his office said.
Lawmakers Amin Sherri and Muhammad Hasan Raad were accused of "exploiting Lebanon's political and financial system" to benefit Hizballah, according to a statement from the US Treasury.
Berri said the unprecedented sanctions constitute "an aggression against parliament and certainly an aggression against Lebanon".
Berri's Amal Movement is allied with Hizballah, a major political player that took 13 seats in the country's May 2018 parliamentary elections and secured three cabinet posts.
Also placed on the blacklist was Wafiq Safa, a top Hizballah security official close to the movement's leader Hassan Nasrallah.
Hizballah lawmaker Ali Fayyad has deplored the sanctions as "a humiliation for the Lebanese people".
Raises to 50 blacklisted
Washington has upped sanctions against Iran in recent months, as well as Hizballah, which the US considers a terrorist organisation.
The Shia movement "threatens the economic stability and security of Lebanon and the wider region, all at a cost to the Lebanese people", said Sigal Mandelker, the US Treasury's under secretary for terrorism and financial intelligence.
The latest sanctions brought to 50 the number of Hizballah individuals and entities blacklisted by the Treasury since 2017.
This "maximum pressure campaign against the Iranian regime... and its proxies has already succeeded in limiting the financial support Hezbollah receives", US Secretary of State Mike Pompeo said on Tuesday.
The US unilaterally pulled out of a 2015 nuclear accord between Iran and world powers in May last year and reimposed biting sanctions.
Sherri, 62, was elected as a lawmaker for Beirut in 2005, and again in 2018.
Close to Hezbollah's security apparatus, he has also been accused of having "threatened Lebanese bank officials and their family members" after the freezing of bank accounts of Hizballah members placed on the US sanctions list, the Treasury said in a statement.
In the statement, Sherri appears in a photo next to Ghassem Soleimani, who heads the Quds Force, Iran's Revolutionary Guard unit for external operations.
Raad, for his part, is head of Hizballah's parliamentary group and a "veteran" of the party.
He was first elected to parliament in 1992, in the first polls held after the civil war that ravaged the country from 1975 to 1990.
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