Barnes picked up the foot injury in the 8-0 demolition of Sheffield United in the Premier League on Sunday.
It was just his second start for the Magpies since switching from Leicester City for £38m in the summer but Barnes lasted a little over ten minutes before going off injured to be replaced by Anthony Gordon.
Head coach Eddie Howe said: "We think he's going to be out for around three months. No surgery required, which is good news, but his foot is now in a boot.
"It is an injury underneath his toe and he's now started his recovery. I think he's going to be quite sedate for a period of time because he's got to rest the toe, he's got to give it every chance to recover and then we'll have to build him up slowly, so that's why it's the three months."
Asked how England international Barnes had taken the news, Howe said: "He's a very stable, level lad; he's a great character.
"Yes, he's hugely disappointed and frustrated because he wanted to show everybody what he could do here and wanted to contribute.
"He's very recently a new dad, which is a great moment in his life.
"I always say when these things happen you have to try and draw the positives, and he'll have the chance to be with his family maybe a bit more than he would have been.
"Things will settle down and then when he comes back, which will quickly be around the corner, he'll have a big part to play for the rest of the season."
Barnes has scored one goal and provided one assist in six Premier League games this season.
