The Toyota driver managed to clock two fastest stage times from the four completed stages on Friday, following the cancellation of Stage 3 and Stage 7.
Evans earned a share of the lead with Hyundai’s Thierry Neuville after the morning loop, before pulling out a 3.0s advantage over the Belgian in the afternoon.
New world champion Kalle Rovanpera also claimed two stage wins to head into Saturday’s leg in third, 5.1s adrift of team-mate Evans.
Hyundai’s Ott Tanak completed Friday’s reduced leg in fourth, (13.9s), ahead of home hero Takamoto Katsuta (20.9s), and the sole M-Sport Ford of Gus Greensmith (2m00.4s).
Eight-time world champion Sebastien Ogier was almost three minutes behind Evans after suffering a puncture on Stage 2, while Craig Breen and Dani Sordo retired after incidents in the morning.
Organisers shortened the first stage of the afternoon, a repeat of the day’s opening Isegami’s Tunnel test, due to the wreckage of Sordo’s Hyundai following a spectacular fire.
It meant crews stopped short of the famous tunnel that had also caused crews visibility issues due to the dust being kicked up by preceding drivers.
The new look stage was won by Evans, who clocked up his second stage win of the event to move into the outright lead from Neuville.
Neuville managed to keep the pressure on the Welshman in the tricky test, that featured a relentless run of narrow twisty roads, but ended up 1.1s shy of the Toyota driver.
Ogier came through third fastest as he looked to try and recover some of the time lost to a puncture in the same stage earlier in the morning.
After undergoing a transmission repair in midday service, Tanak was back competing at full speed. The Estonian was 3.4s adrift of the pace but was faster than Katsuta, Rovanpera and Greensmith. Tanak would however lose the use of his hybrid unit on the next stage.
Rovanpera ended the day with his second stage win after setting the pace on Stage 6. The Finn, who had been battling understeer during the day, was 0.3s faster than Evans.
Neuville dropped 2.2s to Rovanpera after admitting he was too cautious in the test due to leaves on the road.
"It's getting more and more [full of] leaves,” said Neuville.
“You can't see the road and you don't know what the grip is like underneath them. I struggled in there because I don't want to do a mistake. We are in a good position and we are staying in the fight.”
Ogier was lucky not to add to the time loss he suffered in the morning when he clipped a barrier in Stage 6 that damaged the right side of GR Yaris.
Crews returned to the Toyota Stadium service park after organisers cancelled Stage 7 due to damage caused to the armco barriers caused by Breen’s crash in the morning pass.
The Irishman understeered at a left hander which resulted in his Puma diving through the barrier.
M-Sport is attempting to repair the car to in order to allow Breen to rejoin the rally for Saturday’s leg, featuring seven stages.
In WRC 2, Emil Lindholm heads the field and is on course to secure the title after rival Kajetan Kajetanowicz crashed out of the rally when he misjudged the exit from Isegami’s Tunnel on Friday morning.
