General manager Ray Shero said the decision not to make a qualifying contract offer to Ouellet was driven largely by the salary cap and the fact that Ouellet would be eligible for salary arbitration.
"The decision was not about Michel, but about the system," Shero said. "Michel did a good job and made strides last year. I respect those strides, but I don't believe his (salary range) is where he thinks he might be."
Ouellet has scored 35 goals in the past two seasons, and had 19 goals and 48 points last season.
The Penguins extended qualifying offers to six players who will not become free agents on Sunday as a result. They are forwards Colby Armstrong, Erik Christensen, Maxime Talbot and newly acquired Tim Brent, and defenceman Ryan Whitney and Ryan Lannon.
The Penguins did not make a qualifying offer to goaltender Andrew Penner, who played for the Wilkes-Barre/Scranton farm team last season.