Danell Leyva was the only American who finished better (88.898), placing fourth in Glasgow, Scotland. Whittenburg advanced to this weekend's event finals in still rings (15.466) and vault (15.033) after finishing eighth in both.
"Full day was a bit of a struggle, but that's part of the process," the Edgewood graduate said in an interview with USA Gymnastics. "Just going to try to get a little bit more redemption going into team finals."
The United States finished fifth in the team qualifying; the top eight countries automatically qualify for the 2016 Summer Games.
"We expect to go to Rio because that's we've worked so hard for," Whittenburg said. "So we're just going to try to focus on the next thing, which is team finals."