After the game Lowry said Stevens also "said a couple vulgar words" to him.
Stevens was later escorted out of the game and Lowry called for him to be banned from all future NBA games.
"Mr. Stevens' behavior last night did not reflect the high standards that we hope to exemplify as an organisation," the Warriors said in a statement.
"We're extremely disappointed in his actions and, along with Mr. Stevens, offer our sincere apology to Kyle Lowry and the Toronto Raptors organisation for this unfortunate misconduct.
"There is no place for such interaction between fans -- or anyone -- and players at an NBA game.
The 60-year-old Stevens, who joined the Warriors' ownership team in 2013, is a venture capitalist who was a partner with Sequoia Capital until 2012 and is now a managing partner of S-Cubed Capital.
The team said Stevens will not be attending any of the remaining games of the NBA Finals and that a review of the matter is ongoing.
Game Four will be held in Oakland on Friday.
(Reporting by Rory Carroll, editing by Ed Osmond)
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