Collins became the league's first openly gay player when he signed with the Brooklyn Nets last Sunday, and his No. 98 jersey has been the top seller on NBAStore.com. He chose the number in tribute to Shepard, who was killed in an anti-gay hate crime in 1998 in Wyoming.
The former Stanford star had a special meeting Thursday night in Denver. He met privately with Shepard's parents and brother following Brooklyn's win over the Nuggets.
He tweeted a picture captioned, "I'm so fortunate to have met Matthew Shepard's parents and brother tonight after @brooklynnets win tonight in Denver."
Collins also presented them with the No. 98 jersey.
The league says Friday the donations will total no less than $100,000, and it will also auction off Collins' autographed, game-worn jerseys to benefit the same organizations.
Collins says he is thrilled to help the organizations that "work tirelessly to ensure LGBT youth get the resources and assistance they need to be successful in life."
(The Associated Press contributed to this report)