The 23-year-old followed her opening 67 with a sparkling 66 to reach 11 under par, putting her two shots ahead of Australian Whitaker who signed for a 68.
Then came a three-shot gap to Thailand's Nontaya Srisawang and England's Melissa Reid who had scores of 68 and 67 respectively, with Reid's compatriot Laura Davies, who went round in three-under 69, a stroke further back on five-under 139.
Davies partnered Hedwall who is defending her title in Wiener Neustadt this week. Hedwall has shown little indication of the effects of her two-month absence from the tour, caused by a hip injury.
Her comeback event could hardly have gone better, with a round to play, and Hedwall said on ladieseuropeantour.com: "I'm playing very solidly.
"I shot better than yesterday [Friday] and yesterday was good so I'm very happy. The course suits me really well: I love the course. It's in great shape and suits my eye."
Whitaker, 26, is in her first year on the tour and has not had a top-10 finish in 10 events in 2012, but that seems sure to change on Sunday.
"It's been a bit of a grind this season so it's good to get a little momentum going," she said.