Rondo was involved in an acrimonious spat with associate head coach Boylen during and after the Bulls' 107-82 defeat to the Dallas Mavericks on Saturday.
Bulls head coach Fred Hoiberg said Rondo had been suspended for "conduct detrimental to the team" ahead of Monday's clash with the Portland Trail Blazers.
The decision was taken after a discussion between Rondo, 30, and Hoiberg on Sunday. Rondo apologized to coaching staff and team-mates following the meeting.
"Rajon will be suspended for tonight's game for conduct detrimental to the team," Hoiberg said Monday.
"He and I met (Sunday), had a good meeting. He'll meet us at the plane tonight; he'll be back in uniform (Tuesday) against Detroit and moving forward. As far as the details, I'm not going to get in the details of it. We're going to move past it, and again, he'll be back in uniform tomorrow."
Rondo joined the Bulls this year on a two-year deal worth $28 million after spending nine seasons with the Boston Celtics and last season with the Sacramento Kings.