Buxton went on the 10-day disabled list Wednesday as the center fielder continues to have problems with a fractured big left toe.
Santana is still having problems with the middle finger on his pitching hand, which required offseason surgery.
Buxton went on the disabled list on April 18 with a migraine. In his first minor league rehab game, he fouled a ball off his left foot, suffering the hairline fracture.
"It's one of those things where I felt like I could tolerate," Buxton said. "We all felt it would heal over time, but it's something that didn't do as we planned.
"Me, in my opinion, hopefully, I find a better tolerance level; but in reality, it's probably something I need to heal to keep it from lingering around. But I have to see where I set when this stint is over."
Buxton was reinstated on May 10, but he hit .122 with 17 strikeouts and one walk in 49 at-bats over 17 games before landing back on the disabled list.
He was inserted as a pinch runner in the ninth inning Tuesday, but he did not try to steal in the Twins' 2-1 loss in 14 innings to the Kansas City Royals.
"I didn't trust it enough to put pressure on it," Buxton said. "I knew then, if I couldn't steal a base, something isn't right. It's changing the way I'm playing."
He will have his foot re-examined.
"I think that he's been trying to play through something that's been very problematic in terms of mechanics, being able to swing properly, all those types of things," Twins manager Paul Molitor said. "It's taken away some of his aggressiveness as a baserunner and a defender to some degree.
"If we're going to get going in the right direction, he's going to be a part of it, and we want to make sure we get him back on track. We think taking a little break, maybe getting that foot re-examined to make sure that there's no changes in how he has healed to this point."
Santana threw 59 pitches over 3⅓ innings in a Tuesday start for Class A Fort Myers, allowing one run and two hits, in his second minor league rehab start.
Molitor said they are pulling Santana off his rehab because he is dealing with swelling.
"We want to get him back to the surgeon and make sure that we're doing the right things as far as how we're bringing him along," Molitor said.
"We're going to get it examined again, get some more pictures and see, and put together some kind of plan again over the next 10 days and see where it takes us. But I don't know exactly how it's going to go. I think it'll somewhat be determined by what we learn getting it re-examined."
Santana went 16-8 with a 3.28 ERA in 33 starts last season. The 35-year-old is in the final year of a four-year $55 million contract with the Twins.
Minnesota recalled right-hander Aaron Slegers from Triple-A Rochester, where he was 5-2 with a 3.27 ERA. The 6-foot-10 rookie went 0-1 with a 6.46 ERA in four appearances last year with the Twins.