The change, effective immediately, applies only to tournaments on six tours operated under the PGA Tour umbrella.
Long pants will remain required attire for all official competition rounds.
This week's World Golf Championships Mexico Championship and the PGA Puerto Rico Open will be the first tournaments offering golfers the apparel option.
The move follows years of discussions about shorts being worn during non-competition days with positive feedback from players, fans, sponsors and tournaments for the change.
"It makes the guys a lot more comfortable," four-time major winner Rory McIlroy said of wearing shorts. "I don't think there's anything wrong with professional golfers showing the lower half of their leg."
James Hahn, co-chairperson of the PGA Tour Advisory Council, informed PGA players of the rule change in a video posted on Twitter.
Shorts must be knee-length, tailored and neat in appearance. Compression leggings worn under shorts must be solid in color.
PGA Tour caddies were first allowed to wear shorts during competition days in 1999.
The European Tour began a policy for players wearing shorts in practice rounds in 2016.
The PGA of America has allowed players to wear shorts for practice rounds at the PGA Championship the past two years.
Tiger Woods, a 14-time major winner, said he would welcome the chance to wear shorts in practice rounds in a Facebook Live interview last year.
"I would love it," Woods said. "We play in some of the hottest climates on the planet. We usually travel with the sun and a lot of our events are played in the summer."
Woods will have his chance to don shorts for the first time in a practice round at the WGC event in Mexico on Tuesday.