This development comes after the Black Star went under the knife on Saturday to correct a shoulder injury picked up while playing against Sheffield Wednesday.
The full-back is, thus, ruled out of the Tykes' away trip to Wigan Athletic on Thursday.
"With Andy we had the slot booked for him on Saturday," Heckingbottom told the club's official website.
“We spoke after the last home game, he’d spoken to all the surgeons and specialists and it was looking like we’d have it done and we’ve got another season next season.
"That will be even harder and I’m keen to make sure Yids [Yiadom] is back fit for pre-season.
"Yids wanted to keep playing if he could but there’s still too much of a risk of it popping out.
"[He] wouldn’t have been able to play until the last two games of the season and it’s a sensible decision to take it."
Yiadom has been one of the most consistent names on Heckingbottom's team sheet this season, making 32 league appearances involving 31 starts.
The defender has recently been linked to Premier League outfit Swansea City, with a possible summer move on the cards.
It is unclear whether Yiadom will be fit in time for Ghana's 2019 Afcon qualifier against Ethiopia in June.