Anthony Levandowski, previously worked on self-driving car technology at Waymo, owned by Alphabet.
He is accused of downloading 14,000 confidential files before leaving the company in 2016.
Uber denies it is using stolen technology.
In a court filing last month, Uber maintained its technology is different. It described the claim that employees brought files to Uber with the goal of creating "copycat" technology as "demonstrably false."
Mr. Levandowski has declined to testify in the case, launched in February.
The firing was confirmed by an Uber spokeswoman, who said it was effective Tuesday.
Mr Levandowski had already been removed from working on the self-driving car technology at the heart of the suit.
He started working at Uber in August 2016, when the firm bought Otto, the self-driving truck start-up he had created in the six months after leaving Google.
He declined to testify earlier this year, citing his right to avoid self-incrimination.
Uber maintains its technology is different to Waymo's and says there isn't evidence the files are on its servers. But its search did not include Mr Levandowski's computer.
Judge William Alsup, who is overseeing the case in San Francisco, earlier ordered Uber to return the thousands of "pilfered" files in question by the end of the month.
A spokeswoman for Uber said the firing occurred after Mr Levandowski failed to meet the deadline that would allow Uber to cooperate with the judge's order.
Word of the firing was sent to employees on Tuesday.
Attorneys for Mr Levandowski could not be reached for comment immediately.
Uber has fired the engineer accused of stealing secrets from Google-owner Alphabet after he failed to assist with an investigation related to the lawsuit.