Wickmayer, 20, overcame a nervous start to beat the top-seeded Italian in just 74 minutes and claim her second WTA Tour title.
The Belgian dropped serve after double-faulting twice in the opening game but, after trailing 2-0, won 12 of the next 15 games for an emphatic victory. She won the $220,000 tournament without dropping a set in five matches.
"She was just too good for me today," said Pennetta, who was appearing in her 17th tour final. "She deserved to win, she's played unbelievable all week."
Wickmayer was a late wild-card entrant to the Auckland tournament after a court in Belgium last month lifted a ban she had received for three violations of the World Anti-Doping Agency's whereabouts rule. She is appealing the penalty to the Court of Arbitration for Sport, the European Commission and the European Court for Human Rights.
Wickmayer came under the whereabouts rule when she lifted her world ranking through 2009 into the world's top 50. She was ranked No. 16 _ Pennetta is No. 12 _ at the time she entered the Auckland tournament.
The regulation requires top-50 players to report their whereabouts to anti-doping authorities 365 days a year. Wickmayer blamed poor communication, saying the Flemish anti-doping agency sent notices of the breach to her home in Belgium while she was in Australia.
Wickmayer broke Pennetta in the first, fifth and seventh games of the second set, creating a further eight break-point chances and keeping the Italian under pressure.
Cara Black of Zimbabwe and Liezel Huber of the United States, the world's top doubles combination, teamed to win the doubles final 7-6 (4), 6-2 over Natalie Grandin of South Africa and Laura Granville of the United States.