Manager Andy Green said Jankowski tried to play through the injury after fouling a ball off his foot in Atlanta on April 14. Green said Jankowski would be in a walking boot for a few days and was uncertain how long the outfielder would be sidelined.
Jankowski, known for his speed and defense, was hitting .160 while playing in 17 games. He was drafted in the supplemental first round of the MLB draft out of Stony Brook University in 2012.
The Padres recalled outfielder Jabari Blash from Triple-A El Paso to take Jankowski's roster spot.