Pierre Gasly and Brendon Hartley are already eating through their engine allowance for the 2018 season, with Honda forced to change elements on both Toro Rosso cars.
Gasly became the first victim of the Honda curse this season after his engine went up in smoke at the Australian Grand Prix.
As a result, the MGU-H, turbocharger and the ICE have all been replaced ahead of round two in Bahrain.
Although Hartley was able to keep to his Toro Rosso running at Albert Park, a modified MGU-H and turbocharger have been fitted to his car.
Honda's new F1 technical director, Toyoharu Tanabe, said: "Replacing components for the second race is obviously a difficult decision and not ideal, given that the number of Power Units and ancillary components is now limited to just three per season.
"However we believe this is the right way forward and we will continue our development in order to ensure the same issue does not reoccur.
"Although Sakhir is a tough track for the PU, we hope to move on from this difficult moment, as we focus on this race and those that follow."
The changes mean Gasly and Hartley are already onto their second MGU-H and turbocharger, with Gasly onto his second ICE, too.
The limit before penalties are enforced is just three, while the MGU-K, energy store and control electronics are restricted to two for the season.