Harper and his wife, Kayla, announced on social media that they were expecting their third child back on March 26.
The post was captioned "3 for 3," referencing the number he has worn since coming to the Phillies in 2019.
To fill his spot on the roster, the Phillies have recalled infielder Kody Clemens from triple-A Lehigh Valley.
The Phillies note that Harper, 31, played his 600th game with the Phillies on Friday.
The team is coming off a three-game sweep of the Chicago White Sox.
Harper has been a key piece of the Phillies' offense during their six-game winning streak. They finished the recent homestand with an 8-2 record.
The Phillies are in Cincinnati on Monday for the start of a 10-game road trip that includes three games in San Diego and three in Los Angeles against the Angels.
Per MLB rules, Harper could return to the team for the series finale on Thursday afternoon.