Neuville completed the rally's first loop of gravel stages with a slender 2.0s advantage ahead of overnight leader Rovanpera, who impressed despite starting first on the road.
Toyota's Sebastien Ogier, on his WRC return, reached the morning tyre fitting zone in third (+4.6s) ahead of M-Sport's Ott Tanak (+8.3), with title contender Elfyn Evans in fifth, 12.5s adrift.
Hyundai's Esapekka Lappi (+14.0s) and Dani Sordo (+15.7s), followed by Toyota's Takamoto Katsuta (+18.3s) rounded out the top eight, while M-Sport's Pierre-Louis Loubet retired before tackling the day's opening stage.
The opening stage of the day was held in surprisingly dry conditions considering the deluge that Storm Daniel delivered prior to the rally start. Officials elected to shorten the stage by 7.5kms on Thursday night due to the heavy rain and floods that had damaged a section of the gravel stage.
Crews had expected far wetter conditions but were greeted by a relatively dry road, although the rain had exposed plenty of rough bedrock. It was bad news for overnight leader Rovanpera, who started first on the road.
The Finn was able to limit the effects of road cleaning to post the fifth fastest time on the test, 5.5s adrift of the pace, but he dropped to fourth overall.
After the cancellation of Thursday's Lamia shakedown stage, it was Neuville who appeared to have made the best gamble on set-up as the Belgian won the 10.37km Loutraki test by 3.4s from Ogier.
"We need to work a bit on the car, without shakedown there's a few small adjustments to do," said Neuville.
Tanak was third fastest, half a second adrift of Ogier, but the Estonian admitted his M-Sport Puma was "not easy to drive".
After dropping 2.8s in Thursday night's super special stage, Evans lost a further 4.2s in the rally's first gravel test. The Welshman reached the stage end with his right rear tyre off the rim.
Sordo edged Hyundai team-mate Lappi, who was shocked by a lack of pace to finish 6.8s behind Neuville. Toyota's Katsuta, who was the only Rally1 driver unable to complete a pre-event test in Greece due to wildfires, was ninth fastest after a cautious run.
There was, however, drama for M-Sport's Loubet, who ground to a halt on a road section before the start of stage two with a technical issue on his Puma. Loubet and co-driver Nicolas Gilsoul were forced to retire from the day after failing to revive the car.
In WRC2, championship leader Andreas Mikkelsen suffered a delaminated right rear tyre while title contender Oliver Solberg lost 3m31s to a fuel pump problem.
The final stage of the loop (Pissia, 16,3km) featured much more of a challenge to drivers on two fronts. The road was predominately dry, albeit punctuated by several large puddles in places, but it was a severe compression that caused plenty of drama.
Rovanpera was the first to encounter the conditions and the compression which pitched his GR Yaris into the air and onto its nose briefly. Somehow he wrestled the car back before going on to record a stunning stage win.
"We had a huge moment on this one - a dip which was much worse than on the recce," said Rovanpera. "The impact was huge so it threw the car everywhere."
The Finn climbed to second overall after beating rally leader Neuville by 3.1s through the test, as the Belgian admitted he was taking it steady over the compressions.
Ogier completed the stage, 0.3s slower than Neuville but quicker than Tanak (+7.2s), Evans (+9.0s), Lappi (+10.4s), Katsuta (+11.3s) and Sordo (+12.3s). Lappi and Katsuta were however fortunate not to roll their cars after hitting the compression that almost caught out Rovanpera.
In WRC2, M-Sport's Adrien Fourmaux led Nikolay Gryazin by 3.4s. Mikkelsen lost more time when his left rear tyre came off the rim while Solberg continued to battle with a fuel pump issue.
A second pass through Loutraki followed by runs through Livadia (21.03km) and Elatia (28.32km) will complete Friday's action.
