The group crossed into Mexico on Friday. One of the two found alive is injured.
The survivors -- Eric James Williams and Latavia "Tay" McGee -- have returned to the U.S., their families said.
The four Americans -- Williams, McGee, Zindell Brown and McGee's cousin Shaeed Woodard -- arrived Friday morning in Matamoros, Mexico, which is in the northeastern state of Tamaulipas just south of Brownsville, Texas.
"Shortly after crossing into Mexico, unidentified gunmen shot the passengers of the vehicle," the U.S. Embassy in Mexico City said. The Americans had been traveling in a white minivan.
"The gunmen herded the four U.S. citizens into another vehicle and fled," the embassy said.
The Americans were not directly targeted, Attorney General of Tamaulipas, Irving Barrios, said at a news conference.
It "seems to be that it was a misunderstanding," Barrios said.
Mexican investigators believe the kidnappers may have wrongly believed the Americans were rival human traffickers, a source close to the investigation told ABC News.
The two survivors were found Tuesday morning in a wooden house in the Lagunona area, outside of Matamoros, Mexican officials said at a news conference. One of the deceased was also found inside the house, and the second was found outside it, a source close to the investigation told ABC News.
Williams had a gunshot wound to his leg, said the governor of Tamaulipas, Américo Villarreal.
The bodies of the two deceased Americans will be transferred to the U.S. on Tuesday, Mexican officials said. The State Department is "in the process" of repatriating the two deceased victims, spokesperson Ned Price said Tuesday afternoon.
Autopsies will be conducted on the two victims who were killed, a source close to the investigation told ABC News.
National Security Council spokesperson John Kirby told reporters Tuesday, "We offer our deepest condolences to the friends and families of those who were killed in these attacks."
