"It's unacceptable to start a period like that," defenseman Luke Schenn said, adding the Flyers "sat back too much" early in the third period.
"I don't think we competed as hard in the third as we did in the second," said winger Wayne Simmonds, who had a pair of goals. "They just looked like they wanted it more than us."
Ryan Johansen scored his second goal of the night, this one from the right circle, to make it 5-2 with 7:38 to go.
Emery has allowed 11 goals in his last two starts.
The Flyers (16-16-4), who fell out of third place in the Metropolitan Division, sorely missed crease-clearing defenseman Nick Grossmann (flu) as Columbus had traffic in front of Emery most of the night.
The Flyers came within inches of facing a 3-0 deficit, but Brandon Dubinsky's shot hit the crossbar late in the second period, and the Flyers scored on the ensuing rush down ice - Simmonds beat goalie Curtis McElhinney with a shot from the high slot.
Just 20 seconds later, Sean Couturier scored with two minutes left in the second period, tying the game at 2 after taking a bouncing feed from Matt Read in front.
"We came back with a flurry at the end of the second, and we were excited going into the third," Emery said. "It's frustrating. Those shots found their way through."
Most of the Blue Jackets' goals came because there was traffic in front.
"I've got to battle and try to find them," Emery said of the shots.
Coach Craig Berube, whose team lost defenseman Erik Gustafsson to a third-period leg injury - he will be reevaluated Sunday - blamed turnovers and the forwards' inability to block shots for the loss.
Former Flyer RJ Umberger had two goals, including an empty-netter, for Columbus.
Jackets winger Marian Gaborik was hit by Zac Rinaldo and left the ice midway through the first period. Gaborik, who had missed the previous 17 games with a knee injury, suffered a broken collarbone.
Rinaldo appeared to hit Gaborik with his elbow, and the Columbus winger fell into Braydon Coburn. Rinaldo could have a disciplinary hearing with the league.
Most of the game was played with one referee. Referee Dan O'Rourke was injured in a first-period collision - he reportedly was coughing up blood after taking a skate to the chest - and did not return.
On Thursday, the Flyers overcame a 3-0 deficit by scoring five third-period goals in a 5-4 win over the Jackets.