This is not the first time the United States attorney’s office has been involved in the case. Earlier in the year, Judge Alsup, citing what he said was compelling evidence against Mr. Levandowski connected to the theft of trade secrets, referred the matter to federal authorities.

In May, Uber fired Mr. Levandowski after he failed to turn over evidence related to the suit, citing his Fifth Amendment right not to incriminate himself.

An Uber spokeswoman said nothing that Mr. Jacobs said on Tuesday impacted the merits of the case against the company. “Jacobs himself said on the stand today that he was not aware of any Waymo trade secrets being stolen,” said Chelsea Kohler, the company spokeswoman.

The systems Mr. Jacobs described seemed to mirror those uncovered by reporters over the last year. In April, it was revealed that Uber used an elaborate system to track and sabotage Lyft, a top competitor in the ride-hailing business.

The program, known inside Uber as Hell, helped the company locate drivers who also drove for Lyft, allowing it to offer financial incentives to get drivers to work for Uber instead of Lyft. They used software that was developed by a group known inside Uber as COIN, short for “competitive intelligence.” The Federal Bureau of Investigation is investigating Uber’s business practices regarding the Hell program.

The letter from Mr. Jacobs’s lawyer, parts of which were read in court, also said three Uber employees had gone to Pittsburgh to instruct the company’s autonomous vehicle group, which is testing self-driving cars in the city. The research group was told to use the special communication practices with the Uber security group to prevent sensitive information from emerging in potential legal disputes.

Mr. Jacobs said in testimony on Tuesday that an outside company had supplied Uber with devices for hiding communications. The company also ran a separate effort to hide communications via Wickr, a service that deletes communications after a given amount of time, he said.