When the ad break finished, the German rider was on - which meant viewers missed the end of the British round without learning the result.
The poorly timed ad break has angered some viewers, who took to Twitter to vent their frustration.
Listener writer Toby Manhire was among those who was unimpressed, tweeting: "Sky cut to ad break during climax of equestrian, while Prime showing it live. #skyunderclass''.
Kirsten McKenzie - writing all in capitals to convey her dismay - questioned what had happened to the equestrian coverage.
"I haven't stayed up till now for you to advertise your own programming,'' she tweeted.
Another user said the coverage was an "epic fail''.
Sky TV spokeswoman Kirsty Way said it was "unfortunate'' that the Olympic Broadcast Services feed the broadcaster relied on became unavailable.
"That's something that's completely out of our control, and wouldn't have affected only Sky,'' she told APNZ.
"We understand the disappointment. It's very unfortunate that there was a break in the excitement of the feed, but unfortunately these things do happen.''
Ms Way said the issue was not limited to New Zealand, with Foxtel in Australia also having problems with the feed.
"We restored coverage as soon as we were able, and we did elect go to an ad break on Sky as we were unsure how long the loss would be for.
"When coverage on Sky resumed with no commentary we ran a crawler message advising commentary would continue shortly.''
Ms Way noted a similar problem happened during the 2008 Beijing Olympics, when TVNZ's coverage blacked out during swimmer Moss Burmester's epic effort in the 200 metres butterfly.
"It's just unfortunate. It's possibly more likely to happen when we've got eight or nine different channels compared to just one.
"But I think without focussing on this small outage, overall the coverage has been outstanding and there's such a huge selection for New Zealanders.''
Ms Way could not give details on why Prime TV persevered with its coverage while Sky cut to ads, saying she was still looking into what each channel did.
But she added: "We have some options of what we can do. It's our preference not to have a black screen, so that's why we would have switched to some ads.''