Philipsen finished second in each of the Turkish tour's opening two stages but timed his burst perfectly in Izmir to leap above Groves in the overall standings.
It was an impressive performance from the 24-year-old, who now holds a two-second lead over the Australian heading into the mountains for Stage 4.
"If I was second again today, it'd have been sh*t but two times second and a win is good," Philipsen said after the race.
"Maybe my sprint is not on the best level yet. But we've got some time to do some sprints and then go towards the Tour de France with some speed in our legs."
The third stage saw riders navigate the Aegean coastline on a 117.9-kilometre course from Cesme to Izmir, and it didn't take long for the first breakaway to form.
Noah Granigan (Wildlife Generation), Vitaliy Buts (Sakarya BB), Peio Goikoetxea (Euskaltel-Euskadi), Umberto Poli (Novo Nordisk), Leo Bouvier (Bike Aid) and Scott McGill (Wildlife Generation) all made their move with mountain and sprint classifications in mind, though the peloton ensured the gap never got beyond two minutes.
Granigan was the first to the top of the categorised climb 28 kilometres in but the break eventually evaporated with 30 kilometres remaining after Lotto Soudal, Alpecin-Fenix and BikeExchange-Jayco set the pace for the chase.
Bouvier and McGill were the last to be caught after Goikoetxea crashed on a turn; setting up what looked to be another sprint finish.
Jay Vine (Alpecin-Fenix) then fell victim to a crash inside the final three kilometres, but that didn't deter the sprint teams up front, with Team DSM attempting to control the last kilometre for Alberto Dainese.
The wide road and considerable tailwind didn't help Dainese's cause and his rivals soon made their move, as Philipsen launched himself off the wheel of Groves and across the finish line.
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