The Astros will make a corresponding roster move on Friday.
"It still hurts and I might be on the DL, but I don't know if I'm going to be able to play after the 15 days," Gonzalez said. "It's just a bruise, but it hurts for now."
Gonzalez is the third Astros position player to go on the DL in less than a week, joining outfielders Travis Buck (right Achilles' tendinitis) and Carlos Lee (left hamstring strain).
Gonzalez was examined by a foot specialist and underwent X-rays after he reported to Minute Maid Park on Thursday with a swollen right foot. Gonzalez, a Rule 5 pick last year, is hitting .261 with one homer and three RBIs in 69 at-bats.
"He came in and was a little tender," Astros manager Brad Mills said. "We took him to get some X-rays and see a doctor. I think it was a little more swollen than we anticipated and that's why we wanted to have a foot doctor check him out."
Center fielder Jordan Schafer returned to the lineup after being held out of the starting lineup the previous two games with an illness. Schafer served as a pinch-runner late in Wednesday's game.
"He's going to have the sniffles and coughs like we all do when you on the back end of a situation like that," Mills said.