Harris will stay on the weekend edition of "Good Morning America," which he has co-anchored since 2010.
Harris joined ABC News 13 years ago. Since then, he has covered mass shootings, natural disasters and global trouble spots, reporting from Iraq on six occasions. ABC News president Ben Sherwood called him one of the network's "most versatile anchors."
Harris will be joining Cynthia McFadden and Dan Abrams at the anchor desk of the late-night news program.
ABC News says Weir is leaving the network for an undisclosed job elsewhere in the news industry. He has been a "Nightline" co-anchor since 2010 and is a former co-anchor of the weekend "GMA."
"Nightline" airs weeknights at 12:35 a.m. ET.
The Associated Press contributed to this report.