The 23-year-old Welshman suffered a leg injury in training, which will keep him out for six weeks.
Howe has said that he hopes to develop Partington, who has played as a midfielder for most of his career, into a defender next season.
"Hopefully this will be the start of an exciting journey for him. We've been really pleased with him," the Cherries boss told BBC Radio Solent.
"He is developing really well and it is a blow to lose him. It's a real shame for him because he has developed from what we have seen in training into a really good centre-half.
"The only thing holding him back here is the competition he faces from other players."
Partington has played 18 times for Bournemouth this season.