Verstappen took pole position for Red Bull for the F1 season opener and led the opening stages of the race, but frequently reported problems and was unable to pull more than two seconds clear of Lewis Hamilton.
This allowed Hamilton to pit early and get the undercut on Verstappen, laying the foundations for the Mercedes driver to win the race by 0.7 seconds following a late battle.
Red Bull F1 advisor Marko said the differential issue in the opening stages was costing Verstappen around three-tenths of a second per lap, with teammate Sergio Perez managing a similar issue on his car.
"What was most serious at the beginning of the race was that there were problems in the differential area," Marko said in an exclusive interview with Motorsport.com's German language sister site formel1.de.
"In Sector 1, we lost drastically, up to three tenths per lap. The same was the case with Perez, by the way. Not only was there less grip, but the rear wheels were spinning and the tyres were getting hot.
"During this phase, we didn't manage to gain the advantage we would have needed to avoid an undercut. We fell back from 2.5 to 1.7 seconds. That was the decisive phase of the first stint, where we were clearly handicapped.
"And then we had another problem, namely that we had to turn down the engine power due to temperature problems. But Max still managed to catch up."
Verstappen was able to catch Hamilton in the closing stages thanks to a tyre advantage, but made an overtake off-track at Turn 4 and was asked to give the position back.
Hamilton was then able to keep Verstappen at bay and prevent him from making a second overtake, ensuring Mercedes made a winning start to the season.
Despite missing out on the race win, the performance nevertheless marked Red Bull's strongest start to a season for a number of years, giving the team hope of mounting a sustained title challenge.
Looking ahead to the second race of the year at Imola, Marko said that even with a strong car and power unit package, Red Bull would still have to perform flawlessly to defeat Mercedes.
"I think with the package we have, a very competitive engine, a chassis that reacts well to everything, that we will be back on par with Mercedes," Marko said.
"We know now, you can only succeed against Mercedes if you act flawlessly. Everything has to be right.
"We assume that it will be a similar situation - hopefully with a reversed podium and Max on top."