Shelvey had a hand in the first of Dwight Gayle's two first-half goals.
Newcastle had looked comfortable, and were repeatedly hitting the home side on the break, when Shelvey missed a glorious chance in the 79th minute.
Ayoze Perez had also missed a chance to put the visitors 3-0 up.
Bournemouth quickly pulled a goal back and former United midfielder Dan Gosling netted an 89th-minute equaliser.
Asked about Shelvey's miss, manager Benitez said: “Everybody is disappointed, especially him. He knows it was a good chance.
"It’s something that can happen, and the important thing is to make sure that the team remains as strong as it was in the first half.
"We had control for most of the second half, and the good thing is that we continued to create chances. We did a lot of things right, but we didn’t win the game.
“I wasn’t worried about missing the chance, but afterwards when we conceded the goal, I could feel that things were changing.
"We had to manage things better, although it was difficult because they were pushing and making crosses from everywhere.
"You have to defend that. We were trying to clear, but we couldn’t because they were getting the second ball. You have to defend that though, and you have defend better.
"We didn’t do that, and after 70 minutes of doing well, we couldn’t defend well enough."
The result saw Newcastle drop down to 15th in the Premier League.
Benitez's side are two points above the relegation zone.