The retaking of the airport was a victory for leaders of a province fighting for greater autonomy from the socialist central government.
Soldiers and military police melted away before the protesters flooded into Santa Cruz's Viru Viru airport, avoiding clashes. It was not immediately clear if the troops had left the airport entirely or withdrawn to a distant part of the facility.
Morales ordered 220 troops to take control of the airport Thursday after workers threatened to block flights that did not pay landing fees to local officials rather than the national airport authority. Among the carriers affected was American Airlines.
The dispute quickly became a flashpoint between Bolivia's national government and a region seeking greater autonomy.
At least two soldiers were wounded Thursday, one by gunfire, and local hospitals reported that about 20 other people were injured, some by tear gas fired by troops to repel protesters shouting, "The airport belongs to Santa Cruz!"
Santa Cruz Gov. Ruben Costas called on residents Friday to retake the airport and thousands responded, marching past startled passengers into the terminal and waving clubs and green-and-white Santa Cruz flags.
The soldiers left "with their tails between their legs," Costas said.
Planes continued to land and take off Friday, though passengers who had boarded one flight had to disembark because the air traffic controllers brought in with the troops had left and the returning old controllers were not yet back.
The flight left later in the day and the head of the local airport authority said operations were back to normal.
Morales' top aide, Juan Ramon Quintana, called the seizure of the airport "a defeat for the people of Santa Cruz and the people of Bolivia." But the government appeared to accept the airport's return to local control, and said it hoped local officials would root out the corruption it said was marring operations at the airport.
Morales said he ordered the intervention after workers detained a Miami-bound American Airlines plane carrying 140 passengers on the runway on Tuesday, demanding landing fees of up to $2,000 paid in cash locally, rather than deposited with the national airport authority.
Quintana said national auditors had discovered that 85 percent of the airport's income was going to salaries, and just 15 percent to maintenance and technical improvements. Auditors also found evidence of possible embezzlement, he said. "It was dangerous for the safety of our main airport," Quintana said.
"Preserving the good image of the airports is an obligation," Morales said. "Viru Viru was doing poorly, making illegal charges."
Among the carriers affected was American Airlines, which canceled two flights through Santa Cruz on Wednesday and one on Thursday, as well as flying a plane out empty of passengers on Tuesday. The airline, a unit of Dallas-based AMR Corp., said it was back to its normal two flights through San Cruz on Friday.
Many Bolivians were stranded outside the country by the crisis. Some U.S. citizens were stuck as well as their outbound flights were delayed or canceled.
The airport conflict has broad political implications because Santa Cruz, the nation's largest and wealthiest province, has resisted moves by Morales' leftist government to nationalize industries and redistribute land and wealth to Bolivia's poor majority.
Santa Cruz, home to soy plantations and cattle ranches, is also the center of Bolivia's energy industry, and some worry about foreign investment now that Morales has forced international companies to increase royalty payments. Its leaders want autonomy from La Paz and a bigger share of their state's natural gas revenues, but Morales needs the cash for desperately poor highland states.
The divide between the regions is so wide they even dispute whether La Paz or Sucre should be Bolivia's capital.
Since it became one of the first agencies in Santa Cruz to win autonomy from the national government in the early 1990s, the local airport authority had traditionally nominated three people to lead it, one of whom was chosen by the national government. Fears of interference grew after national officials installed their own choice to lead the agency three months ago.
Among those stranded for awhile by the crisis was Norman F. Mydske, the Latin America director of the Billy Graham Evangelical Association, who had been trying to catch a connection to Cochabamba, Bolivia's central city, since Tuesday.
"I pray everything goes well," he said.
Reporting by Associated Press Writer Harold Olmos