Foster, the NFL's leading rusher last season, left the field during the first quarter of the game against the 49ers, favoring the left hamstring that he strained early in training camp.
"Looks like we're dealing with the same thing we were dealing with at the start of camp," Kubiak said Sunday. "Hopefully, we can get him back on the rehab train and get him ready for opening day. He'll be day to day."
Foster told the Houston Chronicle after the game that the hamstring " didn't pop or anything like that" and confirmed that it was a re-aggravation of the previous hamstring injury.
"Until he hops back out there, there's a concern," Kubiak said. "But it sounds like we're heading in the right direction."
"4 those sincerely concerned, I'm doing ok & plan 2 B back by opening day," Foster wrote. "4 those worried abt your fantasy team, u ppl are sick."
Kubiak said Derrick Ward, a former 1,000-yard rusher, has the edge over former second-round draft pick Ben Tate for the backup role behind Foster, even though Tate has put up more impressive numbers during the preseason. But Kubiak said he still hasn't made a final decision.
"We're still lining up as Derrick as our No. 2 and Tate as our 3 right now, but there's going to be a lot of football played this week," Kubiak said. "I think they both bring something different to our football team, so I could see us playing three guys on game day. Those things will pan themselves out."
Kubiak also said All-Pro linebacker DeMeco Ryans will return to practice Monday. Ryans didn't travel with the team to San Francisco because of an elbow injury.
Even without Ryans, Houston's first-team defense played well again Saturday night, holding San Francisco to three first downs and 50 total yards in the first half. Through three preseason games, the Texans' revamped defense has produced 14 sacks and seven turnovers and limited opponents to 32 percent efficiency on third downs (12 of 38).
Kubiak credits new defensive coordinator Wade Phillips with the progress, but he also sees more individual playmakers than he did last season.
"It's not like it's one guy having a great preseason," Kubiak said. "It's collectively, as a group, all making plays, just bouncing around."
The Texans play at Minnesota on Thursday before trimming their roster to 53 players. Kubiak will take a close look at his secondary, where he still has 18 players.
Cornerback Johnathan Joseph and safeties Danieal Manning and Glover Quin are locks for the starting lineup on opening day. Veteran Jason Allen has been pushing second-year pro Kareem Jackson on the other side, and Brice McCain and second-round pick Brandon Harris will be in the mix in reserve roles.
Beyond that, no spots are guaranteed. Kubiak expects fourth-round pick Roc Carmichael to return this week after missing time with a shoulder injury, crowding the depth chart even more.
"That's the place in camp we've held up very good health-wise," Kubiak said. "From a numbers standpoint, we're very heavy at that position and have been throughout camp. If they're all standing on Friday morning, a lot of good football players, so we've got to weed through that. You can only keep so many."
Other than Caldwell, though, the starting offensive front has remained intact and performed solidly in the preseason.
"Our first group's been very consistent," Kubiak said. "We've been fortunate with those five guys. They've played a lot of football together, and if they can stay out there together, I think they can be a heck of a group."
The Associated Press contributed to this report.