Orlando, Houston and Memphis have reached agreement on a three-way trade.
After acquiring Tyronn Lue from Milwaukee earlier this month as its first Nelson fill-in, Orlando has managed to land Alston by agreeing to surrender a first-round pick to the Grizzlies.
"Rafer is a starting veteran point guard who shoots the ball well," Magic general manager Otis Smith said in a statement. "He gives us added depth and athleticism in the backcourt . We thank Brian, Adonal and Mike for all of their contributions and wish them all the best."
Smith also announced Nelson underwent season-ending shoulder surgery Thursday afternoon. The procedure was performed by Dr. James Andrews in Birmingham, Ala. The rehabilitation will take 4-6 months. Nelson dislocated his right shoulder and suffered a torn labrum on Feb. 2 vs. Dallas.
The 6-foot-2 Alston practiced with the Rockets on Thursday but left before the session was opened to the media. He was averaging 11.5 points and 5.4 assists this season and had 24 assists in Houston's last two games, both Rockets victories.
The Rockets have wanted Lowry since he came out of Villanova in 2006. Houston was eyeing Lowry then, but took Rudy Gay with the eighth overall pick. Later on draft night, the Rockets traded Gay to Memphis for Shane Battier, but couldn't get Lowry.
"We felt like he's a player who would fit well here, could really contribute" Morey said. "He's going to do exactly what coach [Rick] Adelman tells him to do. We feel like it's a young player who can help us now and who we can build around for the future."
The 6-foot Lowry averaged 7.6 points and 3.6 assists in 49 games for the Grizzlies this season.
Senior NBA writer Marc Stein and the Associated Press contributed to this report.