Venezuelan authorities say the attack on Saturday killed at least 100 people.
The latest drill, which the Venezuelan government said it had authorised as an evacuation drill for possible medical emergencies or disasters, included two MV-22B Osprey aircraft that landed near the US embassy and vessels that entered Venezuelan waters in the Caribbean Sea.
Venezuela's information ministry did not immediately respond to a request for comment.
The US embassy said in a statement it remained "committed to ensuring the implementation" of President Donald Trump's three-phase plan, "particularly the stabilisation of Venezuela".
The embassy said Francis Donovan, commander of the US Southern Command, which oversees US military operations in the Americas, was present in Caracas.
"This keeps us on guard," said Evelyn Rebolledo, 57, an administrator living in the capital.
"A foreign country flying over the city itself, this is new to us and more so coming from the United States, given the current situation and all the turmoil in the country. It leaves us in a state of uncertainty."
Trump's administration has backed the government of Delcy Rodriguez, formerly Maduro's vice president, which has passed laws to open up Venezuela's vast oil reserves and mining resources to the US.
