Treasury official Adam Szubin says the action is aimed at unraveling and disrupting funding schemes exploited by such organizations.
Qatar is an important US ally in the Arab Gulf, hosting American bombers, support aircraft and the forward headquarters for the US Central Command.
US officials say cooperation with Qatari officials to stem terrorist financing networks has improved, but more work is needed.
The US imposed sanctions Wednesday on Sa’d bin Sa’d Muhammad Shariyan Ka’bi and Abd Al-Latif Bin ‘Abdallah Salih Muhammad Kawari.
The action freezes any assets they have under US jurisdiction. Americans are banned from doing business with them.