The 26-year-old suffered the injury minutes from the end of Sunderland' s 1-0 over AFC Wimbledon, returning to the field of play shortly after receiving treatment from the Black Cats' medical team.
Johnson is hopeful that the recurrence will not affect O'Nien's availability, but is eager to ensure his long-term fitness is not affected.
“The physio and doctor have done a great job again," Johnson said.
"With that kind of injury, when they dislocate, the danger is the length of time that the shoulder is out. If that’s three or four hours, that’s a big problem. If it’s 20 seconds, it’s different.
"Hopefully, we’ll be able to get through to the end of the season, but inevitably he’ll probably need that shoulder pinned eventually.
"If he can handle it keeping on coming out and going back in, then we’ll be okay. But it’s a fine line.
"You want to protect him in the long term, but at the same time we need him."
Johnson is also hopeful that Lee Burge will soon be available for selection.
The Sunderland goalkeeper suffered a minor injury late in the warm up on Saturday, and dropped to the bench as Anthony Patterson made his full league debut.
“He was just practising his kicking, and he just felt something on his hip flexor," Johnson said.
"I think he felt he could have gone on and played, but when I saw him walking down the corridor, he was sort of dot-dashing in his stride. I felt it was wise to leave him off.
“I thought Patto did well. I thought his positioning was good. In the first half, he came and grabbed a couple of crosses and his distribution was excellent as well. But of course the players in front of him had to protect him.
"We had a little bit of adversity to get over in the warm-up when Burgey was out, but I felt very comfortable with Patto, and I think he’s proved us all right again with that performance. He was steady, calm, composed and quite mature I’d say given his age."