The Flyers jumped out to a 1-0 lead on a goal by Max Talbot but Bryce Salvador equalized just over two minutes later with his second goal of the postseason.
Three minutes later it was disaster for the Flyers as Ilya Bryzgalov attempted to clear the puck instead hitting Devils forward David Clarkson and bouncing the puck into his own net.
To add insult to injury the goal held up as the winner with Ilya Kovalchuk adding an insurance marker five minutes into the third period.
The win means the Devils return to the Eastern Conference Finals for the first time since 2003 when they defeated the Ottawa Senators in seven games on their way to the Stanley Cup.
The victory was the 107th playoff win for Devils goaltender Martin Brodeur good for second all-time behind record holder Patrick Roy's 151.
With the loss the Flyers record this playoffs when scoring the first goal fell to 1-6 and ended what began as an optimistic playoffs following a first round victory over bitter rivals the Pittsburgh Penguins.
The questions will now abound for the Flyers who underwent an offseason makeover trading away captain Mike Richards, fellow star Jeff Carter and signing goaltender Ilya Bryzgalov to a lucrative long-term contract. The second round exit is the second consecutive for the Flyers since they lost in the 2010 Stanley Cup Finals to the Chicago Blackhawks.
New Jersey now awaits either the New York Rangers or the Washington Capitals. Those teams will renew hostilities tomorrow in Washington with game seven falling on Saturday should that be necessary.