The 29-year-old German pounced to secure the stage win at the head of a bunch of 43 riders in a thrilling sprint.
It was a clinical performance from the Lotto-Belisol rider, who prevailed on the 185km route from Kemer to Alanya.
"The Tour of Turkey is a nice race, it is getting bigger every year and it is lucky to have all these great sprinters coming here to prepare for the Giro," he said.
"It's not often that you have a race like this with most of the greatest sprinters in the world. I'm here to start my preparation for the rest of the season leading up to the Tour de France and it's a good start."
Matthew Goss (GreenEDGE) was second, as he was in Sunday's opener, and now leads the overall standings by two seconds from Greipel.
"I'd rather have the stage win than the jersey but I'm happy to be in the lead," Goss said.
"We came here as a team to try and work out the lead out and that's going pretty well. Brett Lancaster did a fantastic job from 1km out but Andre got that jump and I couldn't shut that gap back down."
Matteo Pellucchi of Europcar is six seconds further back after finishing third on the stage, as is Theo Bos of Rabobank, who finished 101st and in the second group.
"To finish just behind such great sprinters like Greipel and Goss can only make me happy," he said.
The stage win was Greipel’s sixth success this season.
On Tuesday, the riders embark upon a 148km trek from Tekirova to Elmali with the finish at 1,800m altitude.
The Tour of Turkey has eight stages. The race finishes with a stage in Istanbul on Sunday.