US President Barack Obama and Attorney General Eric Holder condemned the attack on the officers, who were treated at a local hospital and released, as a law enforcement team in tactical gear swarmed a home in the St. Louis suburb.
Television images showed officers on the roof breaking into the attic with heavy tools.
Shawn McGuire, a St. Louis County police spokesman, said an undisclosed number of people were taken from the house but there have been no arrests so far. He would not confirm media reports that two men and a woman were led away.
Long-simmering tensions between African-Americans and Ferguson's mostly white police force came to a boil in August when a white policeman killed an unarmed black teenager. The shooting of 18-year-old Michael Brown led to a coast-to-coast wave of demonstrations last year.
The rally at Ferguson police headquarters on Wednesday evening was called hours after the resignation of its long-criticized police chief, Tom Jackson, but activists demanded more changes. Jackson quit in the wake of a scathing US Justice Department report that found his force was rife with racial bias.
Around midnight, gunfire rang out, leaving a 41-year-old St. Louis County Police officer with a shoulder wound and a 32-year- old officer from nearby Webster Groves Police Department with a bullet lodged near his ear, St. Louis County Police Chief Jon Belmar said.
"This is really an ambush, is what it is," Belmar said of the shootings, the worst outbreak of violence in the city since riots that broke out in November after the announcement that a grand jury decided against indicting the officer who killed Brown.
The shootings were "inexcusable and repugnant," Holder said in a statement. The White House sent a Tweet that read: "Violence against police is unacceptable. Our prayers are with the officers in MO. Path to justice is one all of us must travel together."
Belmar told a news conference authorities had possible leads, and said the shooter used a handgun and shell casings had been recovered.
"This is No. 1 priority of St. Louis County police to identify that individual or individuals," said Belmar, who leads the police force in the county that includes Ferguson. Officers did not return fire but may in future, he said.
"I have said all along that we cannot sustain this forever without problems," he said, referring to festering tensions in the city since Brown's death.
The shooting came less than three months after a man ambushed two New York City patrolmen, saying he sought to avenge the killings of Brown and an unarmed black man in New York. In both cases, grand juries decided against bringing criminal charges.
"We reject any kind of violence directed toward members of law enforcement," Brown's family said in a statement. "We specifically denounce the actions of stand-alone agitators who unsuccessfully attempt to derail the otherwise peaceful and non-violent movement that has emerged throughout this nation to confront police brutality."
Police and protesters appeared to disagree about where the shots came from, with Belmar asserting they came from the middle of the crowd gathered in front of police headquarters.
"I don't know who did the shooting, ... but somehow they were embedded in that group of folks," Belmar said.
Protesters at the scene insisted on social media that the shots came from further away.
"The shooter was not with the protesters. The shooter was atop the hill," activist DeRay McKesson said on Twitter.
"I was here. I saw the officer fall. The shot came from at least 500 feet away from the officers," he said.
A string of Ferguson officials quit after the Justice Department report, which found the city used police as a collection agency, issuing traffic citations to black residents to boost its coffers, resulting in a "toxic environment". Activists want the city mayor, James Knowles, to step down as well.
Rev Osagyefo Sekou, a frequent participant in the protests in Ferguson over the last several months, said he was in the crowd when shots rang out.
"Tensions are high," Sekou said. "We deplore all forms of violence, we are a non-violent movement. But we also deplore the findings of the Department of Justice report and the suffering and the misery that this community has endured."
After the report, Holder said the federal government would demand police reforms in Ferguson, including possibly dismantling the department.
Knowles said on Wednesday he was committed to keeping the department intact, but Belmar, the St. Louis County chief, would not rule out the possibility that the county would take over policing in the town.
After last autumn's rioting, Missouri Gov. Jay Nixon called out thousands of National Guard to patrol the streets of Ferguson and temporarily put the head of the state Highway Patrol in charge of security.
