Lyness was made to pay for a moment of indecision as Northampton's Adebayo Akinfenwa headed home the second-half winner - his 15th goal of the campaign and one which took the Cobblers level on points with Burton and above Albion in the table on goal difference.
Rowett said: "I wouldn't blame Dean, he's been great for us this season. He decided to come for the cross but then got caught in two minds. I was more disappointed with the way the goal went in.
"I'm not disappointed with the performance just that fact that we didn't get a result. We got into some decent areas in the second half but the ball just wouldn't fall for us in the box.
"Like Northampton, we're struggling away from home. I know that's three defeats in a row but we're not playing that badly. We're just a bit unfortunate, whereas at home we're probably getting that bit of luck which you need.
"We're winning our home games and that's keeping us in there. I'm aware that we need to improve on our away form but we couldn't train on Friday because of the snow and that wasn't the ideal preparation for the game."