Santalab was conspicuously absent from the Wanderers squad that lost 3-1 to Arsenal on Saturday night, after falling awkwardly on his shoulder during Tuesday's outing against the Olyroos.
The 34-year-old had a reconstruction in late 2014 and re-injured it early the next year.
"He'll be fine," Popovic said.
"We actually felt it was nothing. Ultimately it won't be anything and we expect him to maybe train Tuesday or Wednesday this week.
"But with the history he's had, another knock there may have been a six-to eight-week injury and that's something we didn't want to risk.
"Obviously it's a big game and we wanted him to play, he wanted to play. But we had to look at the big picture."
Santalab became the club's all-time leading scorer last season, overtaking Mark Bridge on his way to netting 14 goals despite starting only 12 of his 21 appearances.
While Popovic was optimistic about his injury, the boss was far less reassuring on the situation of team-mate Aritz Borda.
Asked about the Spanish defender's absence, the coach simply said 'he wasn't selected', a phrase he's used in the past when players are in the process of being moved out.
Borda has a year left on his contract but has played only one A-League game since round 14 last season, when he was sent off against Melbourne City.
It allowed newly-appointed skipper Robbie Cornthwaite to establish a successful central defensive partnership with Jonathan Aspropotamitis.