Apple today announced that it has sold over one million iPhone 3GS models through Sunday, June 21, the third day after its launch. In addition, six million customers have downloaded the new iPhone 3.0 software in the first five days since its release.

“Customers are voting and the iPhone is winning,” said Steve jobs, Apple’s CEO. “With over 50,000 applications available from Apple’s revolutionary App Store, iPhone momentum is stronger than ever.”

It looks like Steve Jobs statement that “iPhone is winning” is directed at Palm Pre, which was called iPhone killer by many analysts. Palm Pre was launched two weeks earlier and it was estimated that around 50,000 Pre units were sold on launch weekend, almost 20 times less than what Apple sold on iPhone 3GS launch weekend.

iPhone 3GS launch even matched the launch of its much hyped predecessor iPhone 3G, both the devices sold one million units in first three days. However, sales of iPhone 3GS is going on at a faster pace, as the phone was launched in just 8 countries compared to 21 countries last year. Apple will start shipping iPhone 3GS in six more countries including Japan (which was the second biggest market last year) this weekend.

iPhone 3GS is all set to be even bigger hit than iPhone 3G for Apple.