The Toyota Gazoo Racing driver was only fourth-fastest on the brand-new Asuke opener, but hit back immediately on Isegami’s Tunnel before adding another stage win on Inabu / Shitara to reach midday service in control.
Evans leads Toyota team-mate Oliver Solberg, who won the opening stage, with defending Rally Japan winner Sébastien Ogier just 0.5sec further back in third.
“It was difficult to judge the grip again,” said Evans after his decisive run through Isegami’s Tunnel. “I tried to carry speed but it is hard to know.”
Overnight rain left damp patches under the trees and made tyre choice difficult throughout the morning. The opening Asuke test, new for this year’s event, immediately caught out home hero Takamoto Katsuta, who clipped a bank on a slippery right-hander and picked up a left-rear puncture.
Solberg made the best start, edging Sami Pajari by 0.2sec to claim the first stage win of the rally. Ogier was third-fastest, 0.9sec down, with Evans another 0.2sec back in fourth.
But the championship leader responded emphatically on the 24.29km Isegami’s Tunnel stage, going 7.5sec quicker than Solberg and moving into the rally lead by 6.4sec.
Ogier could only manage third-fastest, 16.7sec down on Evans, and pointed to his later road position as the reason for the gap as mud and dirt were dragged onto the road.
“It is start position,” said the nine-time world champion.
Evans then stretched his advantage on Inabu / Shitara, where the opening kilometres were drier before the final section became greasy and difficult to read. Ogier was second-fastest, 1.7sec down, and reached service 18.2sec off the lead.
“There is still a long way to go,” Ogier said. “We will put maximum pressure now on Elfyn.”
Solberg slipped to 11.3sec off the pace on SS3 after encountering deer early in the stage, but remained second overall. Thierry Neuville completed the morning fourth, 28.6sec from the lead, after another loop of battling understeer in his Hyundai i20 N Rally1.
The Belgian stayed on soft tyres for the final stage and admitted the afternoon repeat loop could be difficult.
“The rally is still very long,” Neuville said. “The afternoon loop will be a hell of a ride.”
Pajari ended the loop fifth overall, 32.2sec behind Evans, while Katsuta reached service sixth at 43.8sec. The Japanese driver struggled for confidence after his early puncture and was frustrated again after a brief off on SS3.
Adrien Fourmaux sits seventh after a tough start for Hyundai. The Frenchman spun at a hairpin on Isegami’s Tunnel and dropped 35.6sec to Evans on that stage alone, admitting he had “no grip or balance” in the car.
Hayden Paddon is eighth in the third Hyundai, with M-Sport Ford’s Jon Armstrong ninth. Nikolay Gryazin completes the top 10 overall and leads WRC2 in his Lancia Ypsilon Rally2 after a strong run through Isegami’s Tunnel moved him ahead of early category leader Alejandro Cachón.
The same three stages - Asuke, Isegami’s Tunnel and Inabu / Shitara - are repeated on Friday afternoon.