The 25-year-old was a key figure in the Premier League outfit’s backline last season, starting 31 league matches, but failed to make the bench for his side's 0-0 draw with West Ham on Sunday.
But Pochettino has explained that the Japanese centre-back's absence was down to the form of his fellow defenders, rather than any niggles picked up during the international break.
"We have four centre-halfs, 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, (Dejan) Lovren and (Jose) 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."
Yoshida's sole appearance for Southampton this term came in the 5-1 League Cup victory over Barnsley at the end of August.
However, the former VVV-Venlo star played 90 minutes in both of Japan's recent friendly wins over Guatemala and Ghana.
