Struggling with her serve and conceding the contest with her sixth double-fault, Henin-Hardenne also failed to match the consistency of her opponent in the rallies.
"For sure she played well but I wasn't at my best level," said the Belgian fourth seed.
"I wasn't moving well and I wasn't feeling well physically on the court. I was running a lot and was behind my baseline the whole point and it's difficult to win like this.
"I haven't had the best preparation the last few weeks with my injuries and it's not easy to be in a good rhythm. It's a difficult time for me right now but I'll have to be patient."
Pennetta's win put her into the quarter-finals where she will be joined by Anastasia Myskina who took two hours 29-minutes to beat fellow Russian Dinara Safina 7-6 6-7 7-5.
Myskina, seeded eight, held a match point at 6-5 in the second set, which Safina held off with a powerful serve, and she finally claimed victory on her third match point.
"Dinara played pretty well," Myskina said. "I give her all the credit because she moved well. Her serve was also very good and she knew what she wanted to do, so it was a good one."
Myskina has been criticised in Russia after saying on Tuesday she would step down from the Fed Cup squad next year.
But she insisted on Wednesday it was only to allow young and deserving players the opportunity to compete and she will be ready to return if needed.
Others to make the last eight include defending champion Lindsay Davenport, who brushed aside Italian Francesca Schiavone 6-2 6-2, and Slovak Daniela Hantuchova who beat seventh seed Patty Schnyder of Switzerland 6-4 6-3.
