Hamilton was unable to take part in the final part of qualifying in Sochi after suffering a recurrence of the problems that ruled him out of the entirety of qualifying in China a fortnight ago - which Lowe, executive director (technical) at Mercedes, says 'tainted' any joy the team could take from Nico Rosberg's dominant cruise to pole.
Hamilton is therefore set to line up 10th on the grid on Sunday, although he could yet face a grid penalty if engine components need to be changed. He did at least escape with only a reprimand - his second of the year - after the stewards investigated his failure to follow the mandated route around the bollard when he ran wide at Turn 2 during Q1.
"We've let Lewis down for the second weekend in a row, so our apologies go to him once again," Lowe said.
"A great pole lap for Nico and our congratulations to him on a fantastic performance throughout the weekend so far. Unfortunately, however, our day has been tainted by a failure which deprived Lewis of a shot at pole - and deprived the fans of what would surely have been a thrilling climax to an immensely close battle between our two drivers.
"It's a cruel twist of fate that, out of eight Mercedes-Benz Power Units on the grid, the problem should befall the same driver twice. We've been working very hard over the past couple of weeks to understand what happened in China - but unfortunately there is clearly still more work to be done.
"Our focus for the immediate future, however, is on making sure Lewis' car is in the best possible condition for tomorrow's race to give him the best chance of making the kind of strong recovery we've seen him pull off so many times in the past."
Hamilton urged his team to get to the bottom of the problem, but said he was philosophical about the setback - despite the opportunity for Rosberg to further increase his already sizeable gap at the head of the championship.
"It's obviously not a great feeling to be on the sidelines again - but that's life," Hamilton said. "I knew there was a problem and that it was probably the same failure that I had in China pretty much straight away.
"When it happened in Shanghai it was something we hadn't seen before and now unfortunately it's happened again, so we need to understand it. I've never been superstitious about these things, though, and I never will be. There's nothing I can do about it, so I'll move on and look ahead to the race.
"I don't know where I'm going to start yet - we'll wait to see how that unfolds. But I never give up and I'll give it all I've got to recover whatever I can in the race, like always."