Barkley is expected to be a game-day decision, according to coach Brian Daboll, against the Seattle Seahawks on Monday night at MetLife Stadium.
Thomas is dealing with a hamstring injury that did not respond well at practice earlier in the week. He will miss his third straight game.
Barkley has a high ankle sprain. He has been limited in practice throughout the week after missing Thursday night's loss to the San Francisco 49ers.
The original timetable for the Pro Bowl running back had him missing three games. This would be his second.
"It's tough," Barkley said. "It's one of those things I think I'm doing way better than a lot of people would expect, especially talking to doctors. I feel like I'm further along. But it's frustrating because I'm obviously healing fast, but you want it to be faster. Obviously you want to heal fast and it's tough balancing that. Taking it day by day, just fighting every single day coming in to rehab and trying to get myself back to a place where I can come in and compete at a high level for my team."
Joshua Ezeudu will fill in once again at left tackle for Thomas.
Barkley did individual drills during the early portion of practices open to the media this week. But he did not take many (if any) reps in team drills, according to multiple sources.
That usually leads to that individual not playing.
"Well, we'll see how he looks [Saturday]," Daboll said before the final practice of the week. "He's gotten progressively better. Then it's just a talk with Saquon, where he's at, a talk with the training staff. I think everybody has to be on the same page. "Again, I never want to put a guy out there that is not ready to go. But he has gotten better. I think there is a chance, but we'll see where it's at."
But even Barkley seemed uncertain about his availability this week when he spoke after Saturday's practice.
"I don't know," he said of his chances of playing. "I think I'll have a better answer [Sunday]. A better answer the day after that. That's Monday, right? We'll see."
There is no doubt that Barkley is pushing to return. He understands he's unsigned after this season, and there are some who would be more on the patient side to get back on the field because of it.
Barkley, who signed a revised franchise tag the first day of training camp, doesn't view it that way.
"The reality of it is that, if I can go, if my body is telling me to go out there and play, then, yeah, that is what I'd like to do," Barkley said. "Anyone else that is in this situation, or say if some people were in this situation where they don't have a contract behind them or for business reasons, I respect that too. Probably is a smart thing to do, to be honest.
"But that is not really in my makeup and how I view it. I don't judge nobody if they do that, but for me if my body is able to go, that's when I'll go."
Thomas seemed to have the better chance of making it back for the Seahawks game. He told ESPN this week his chances of returning were "good."
He then partook in Thursday's fully padded practice and it did not go as well as planned. The following day, he was kept inside to work with trainers.
"Just wasn't feeling right," Daboll said. "Didn't practice [Thursday]. He won't make the game."
It's not an especially encouraging sign for the Giants' offensive line, which has struggled. Thomas is one constant, when healthy, after earning All-Pro honors last season. New York will get left guard Ben Bredeson back from a concussion after he missed Thursday's game.
On the defensive side of the ball, outside linebacker Azeez Ojulari (hamstring) will also return. He was not given an injury designation for the contest.