Bernadina, who reached first base on Adrian Gonzalez's error, was hit by a pickoff throw from Boston right-hander Aaron Cook at the Red Sox's JetBlue Park.
Bernadina said later he was feeling better after icing the knee, and Johnson plans to play him Tuesday, when the two clubs play at 3:05 p.m. ET at Nationals Park. Initially, though, Bernadina said he was in pain.
"I got hit right on my knee, on the side of my knee," Bernadina said. "I feel better now. I should be fine."
"I'm going to play him tomorrow," Johnson said of his plans. "I hope it's just a bruise."
Before the game, Johnson said he reserves the right to change his mind, but Bernadina would likely start against the Cubs on Thursday.