The Toyota driver set the pace on the 1.48km asphalt stage, held in front of a bumper crowd that had congregated around the Athens harbour.
The stage was the first competitive running for WRC crews after organisers were forced to cancel the shakedown stage in host city Lamia due to the effects of Storm Daniel.
Torrential rain and thunderstorms have caused flash flooding across Greece but organisers remain confident the rally can continue safely.
Rovanpera wasted little time in getting up to speed on the rally’s opening stage, posting a time 0.3 seconds faster than nearest rival, Hyundai’s Esapekka Lappi.
“I have to hope that the conditions are better for me than they normally are in the dry,” said Rovanpera, who will start Friday’s action first on the road.
“After the disappointment in Finland, I want to do a good rally and we have to fight for it.”
Hyundai’s Thierry Neuville was third fastest, a tenth slower than his team-mate but is feeling confident about his chances.
“I haven’t felt this good for a long time in the car, so I am looking forward,” said Neuville.
“We had great speed in the last two events, that’s for sure and there is more to come.”
Dani Sordo ensured there were three Hyundais in the top four, 0.5s adrift of Rovanpera.
Ott Tanak led M-Sport-Ford’s charge in fifth, 0.6s faster than eight-time world champion Sebastian Ogier, who is making his first WRC start since winning Safari Rally Kenya in June.
Ogier’s Toyota team-mate Takamoto Katsuta posted an identical time to share sixth position.
M-Sport’s Pierre-Louis Loubet was seventh while Elfyn Evans, Rovanpera’s main title rival, could only muster the 12th fastest time, 2.8s shy of the pace.
Evans ended the stage behind WRC2 runners Andreas Mikkelsen, Nikolay Gryazin and Marco Bulacia.
"We have to see what is possible - I don’t think anyone knows what is in front of them, so we just have to deal with it as we see it," said Evans looking ahead to Friday’s stages.
The rally will head 200km north west on Friday as crews prepare to tackle five gravel stages comprising 102km.
