Cerqueira's lawyers said on Tuesday that the suit, which accused the airline of violating his civil rights, was the first of its kind to go to trial. The federal jury in Massachusetts made its decision on Friday.
Michael Kirkpatrick, a lawyer with the Public Citizen Litigation Group, which represented Cerqueira, said: "It's part of this whole debate about security versus civil rights. We don't think there's any conflict between security and civil rights. And the jury came down on our side in this."
Civil-liberties groups such as the American Civil Liberties Union say racial profiling, or ethnic-based targeting, against Middle Easterners has risen in the US since the September 11 attacks.
Two aeroplanes out of Boston, including an American Airlines aircraft, were among the four hijacked in the attacks.
In Cerqueira's incident, police removed him and two Israeli men from a December 28, 2003, flight bound from Boston for Fort Lauderdale, Florida.
The Israelis, whom Cerqueira did not know, had drawn attention by speaking loudly in a non-English language, according to court papers. Cerqueira charged that he was removed from the aircraft with the other two because of their similar "colour and physical appearance".
Police released all three after questioning them for two hours.
Staff of the airline, owned by AMR Corp, then told Cerqueira that the airline would not let him fly, citing remarks he made on the plane. They refunded the ticket cost and suggested Cerqueira, a regular American Airlines flier, find another way home.
David Godkin, a lawyer at Birnbaum & Godkin, a Boston law firm that also represented Cerqueira, said: "Mr Cerqueira was literally just sitting in his seat minding his own business and he was removed from the plane and interrogated, detained for two hours for the sole reason that he appeared to be travelling with two passengers who were seated next to him ... he was caught up in it because of his similar appearance to them."
American Airlines spokesman Tim Wagner said of the verdict: "This decision is simply not supported by the facts or the law. We will evaluate our legal options."
The two Israeli men were also released, but denied further service by the airline, Cerqueira's lawyers said.
Ibrahim Hooper, spokesman for the Council on American-Islamic Relations, a Washington-based advocacy group, said: "The message is clear, that airlines have to treat their passengers fairly, without discrimination, based on religion or ethnicity or perceived religion or ethnicity. Those airlines that fail to do that will pay a financial price."
In other recent incidents, the ACLU accused federal security officials at New York's John F Kennedy airport in August of unfairly targeting Muslim, Arab and South Asian passengers for extra scrutiny.
A US Customs and Border Protection official denied using racial profiling, but said passengers from "high-risk areas" received close attention.
In November, six Muslim imams were removed from a commercial flight in Minnesota after being accused of "suspicious activity" that they said amounted to no more than saying evening prayers.