The Japan international was a key Saints centre-back last season but was not in Pochettino's matchday squad for the weekend's 0-0 draw with West Ham United.
"We have four centre-halves, we have four defenders, it is also clear that Maya was the last one that arrived during the pre-season," he said.
"He had a really tough pre-season, especially at the beginning. Nonetheless, there is four central defenders and only two can play so I have to make those decisions.
"At the moment, Lovren and Fonte are playing, so that's basically it. It doesn't have to be that there is a problem with Maya, there is no problem with Maya Yoshida."