The case has gone up and down the hierarchy of the court system, starting with a 2008 ruling that the jet engine maker had violated the False Claims Act, but did not meet the criteria for damages under common law.
No monetary penalties were assessed in that ruling and both the U.S. Justice Department and the company, which is based in Connecticut, filed appeals.
A federal appeals court in Cleveland later ruled that the company was in violation of the False Claims Act and that the lower court should revisit the issue of whether or not damages should be paid under common law.
Under Thursday's penalties of $364 million were assessed for violations of the False Claims Act and $109 million added to that on common law claims.
The case began with charges that the defense contractor submitted price proposals for F-15 and F-16 fighter jet engines that purposefully used outdated data that would result in smaller totals than would be submitted when the bills came due.
"UTC's proposed prices for the engine contract misrepresented how UTC calculated those prices, resulting in the government paying hundreds of millions more than it otherwise would have paid for the engines," the Justice Department said in a statement.
The case covers the company's behavior between 1985 and 1990, the department said.