Three-time race winner Takumi Takahashi was running a minute and 40 seconds clear of Jonathan Rea on the #10 Kawasaki as the clock hit the four-hour mark, with Nicola Canepa recovering from a sluggish start to put YART Yamaha in a provisional podium position.
But it wasn’t a straightforward first half of the race for the #33 works Honda crew that claimed pole position, with plenty of drama ensuing in the first few hours.
At the start, Takahashi lost a position to the FCC TSR Honda of Josh Hook, who was able to sprint to his bike faster than all his immediate rivals to grab the lead from fourth position. And to make matters worse, Kawasaki's Leon Haslam also found a way past Takahashi on the run down to 130R on the opening lap, demoting the Honda rider to third.
But Takahashi took little time to regain lost ground, immediately repassing the Kawasaki of Haslam into Turn 1 at the start of lap 2 before making a move on Hook prior to 130R.
The timing of Takahashi’s move turned out to be crucial as the safety car was deployed seconds later for a crash involving two satellite Honda bikes earlier in the lap at Spoon Curve.
It was Kosuke Sakumoto who triggered the incident, losing the front end of his Honda Dream bike into the long left-hander and taking an innocent Naomichi Uramoto on the #73 SDG Honda with him into the gravel.
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When the safety car peeled into the pits more than 20 mins later, Takahashi again struggled to hold on to the lead, with a charging Gregg Black on the Yoshimura Suzuki overtaking Haslam and Hook in quick succession before passing Takahashi when he ran slightly wide at Spoon Curve.
It was then Haslam’s turn to grab the top spot, the Kawasaki rider making a successful move on Hook going into the esses on the following lap.
But once again the advantage of the factory Honda bike was evident and Takahashi quickly dispatched Black into 130R before sprinting past Haslam on the main straight to reinstate the status quo.
Once back out in front, the 32-year-old was able to pull clear of his rivals, building an eight-second advantage over Haslam before handing over the bike to Tetsuta Nagashima.
The ex-Moto2 rider carried on the good work of Takahashi and extended the advantage further to 22s before pitting at the start of hour 3 for Iker Lecuona’s first stint at Suzuka.
Kawasaki’s Rea boxed in at the same time as Takakashi to hand over the #10 ZX-10RR to Alex Lowes, but the three-time race winner struggled for pace out of the pits for the next few laps, dropping over 30s behind a rapid Lecuona.
This would end up having major consequences on the race as a pair of safety cars were sent out on track soon after when the #51 I.W NAC Yamaha caught fire after Hinata Nakajima crashed on the entry to the second Degner.
The gap between the leading two riders meant that Lowes picked up the second safety car, falling more than a minute behind Lecuona’s Honda when the action resumed again.
During the fourth hour, Kawasaki was able to match the pace of the Honda for the first time with Rea at the wheel of the ZX-10RR, but the Northern Irishman fell to the ground at the first chicane while navigating his way through traffic.
Rea was able to hop back on his bike again and resume the race, but the 28 seconds he so lost allowed Takahashi to cruise up front and extend his advantage to over 100 seconds.
Some way behind the leading duo, the YART team sits in a net third place after an impressive recovery ride from Canepa, who wasn’t able to get his Yamaha going at the start and dropped to 22nd place.
The Italian was back up to 17th place when the first safety car was deployed at the end of lap 2 before making further headways when the race resumed, snatching the third place where it had qualified just 37 minutes into the race.
However, the YART team's stints have been much shorter than its rivals and it dropped a place for the time being after completing an early fourth stop.
This temporarily elevated FIM Endurance World Championship's point leading Yoshimura Suzuki team from fourth to third, which had qualified down in 22nd after Sylvain Guintoli was unable to take part in a dry first qualifying session due to a hand injury.
With Guintoli returning to the UK to undergo recovery, Black and Kazuki Watanabe are competing as a duo with the former charging to fourth in the opening two laps and even briefly taking the lead after the first SC period, before slipping down three positions.
Fifth place in the race was held for a long time by the FCC TSR Honda team, but a lengthy pitstop where it struggled to change the rear brake dropped it outside the top 10, promoting Takuma Kunimune in the #104 Toho Honda up to fifth.
BMW was running comfortably inside the top 10 until it stopped on track towards the end of the fourth hour, forcing Ilya Mikhalchik to push the bike back to the pits.
