The Astros had a list of four players they could choose from.
Santana, who had been playing at Class A Lakewood in 2011, has been assigned to the Astros' Class A Lexington club. Both Lexington and Lakewood are in the South Atlantic League.
"We're extremely happy," Astros general manager Ed Wade said.
President of baseball operations Tal Smith, Major League scout Paul Ricciarini and special assignment scout Matt Galante each had a chance to watch Santana play recently.
"All three of them were very consistent with regard to how highly they graded Santana, and it was consistent to our previous reports on him that we had gotten through regular pro coverage," Wade said. "He's got plus raw power and a great body, he's a great athlete and a plus arm. He's a tick above-average runner."
The right-handed hitting Santana hit .269 in 96 games at Lakewood with 29 doubles, four triples, seven home runs, 32 RBIs and four stolen bases. He just turned 19, which means he played most of the season in a league with players in their early 20s.
The acquisition of Santana completes the Hunter Pence trade, in which the Astros also received right-hander Jarred Cosart, outfielder Jonathan Singleton and right-hander Josh Zeid.
Cosart and Singleton were ranked as the Phillies' top two prospects by MLB.com and immediately became the top two prospects in the Astros' system.
"As painful as it was to trade someone like Hunter, to get four pretty good prospects is a pretty good day's work for us," Wade said.
Brian McTaggart is a reporter for MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.