Inciarte signed as an international free agent with the Diamondbacks on May 25, 2008, and began his career in the Rookie-class affiliates in 2008 and 2009. He has played in Arizona's minor league affiliates since the 2008 season, hitting .307 with two home runs, 47 runs batted in, and 28 stolen bases in Class-A for the South Bend Silver Hawks as well as Class-A Advanced for the Visalia Rawhide.

The Philadelphia Phillies selected Inciarte from the Diamondbacks with the 15th pick in the 2012 Rule 5 draft. He competed for a spot with the Phillies as a backup outfielder during spring training, and ultimately made their 2013 Opening Day roster. He remained with the Phillies for only one game (in which he did not appear), however, as he was designated for assignment following the team's acquisition of Ezequiel Carrera on April 2. The Diamondbacks reclaimed Inciarte from the Phillies on April 4, and assigned him to the Mobile BayBears of the Class AA Southern League. With Mobile, Inciarte had a .281 batting average, five home runs, 17 doubles, 25 runs batted in, and 43 stolen bases. He appeared in the Southern League All-Star Game. After the season, the Diamondbacks added Inciarte to their 40-man roster.

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