Armstrong was on course for his first race win in the North American single-seater series until he suddenly slowed and was forced to park his car in the run-off.
It was a cruel end to a controlled performance by the Meyer Shank Racing driver, who led 14 laps.
The New Zealander had a comfortable advantage of nearly three seconds over McLaren’s Christian Lundgaard, who inherited the lead and the win after a late Safety Car intervention.
“Racing is sport and sport has its highs and lows,” said Honda Racing Corporation president David Salters.
“We experienced both this weekend. Pole position and four cars in the Firestone Fast Six showed the hard work of our marvelous drivers and teams and our HRC associates yet again.
“In the race we were very competitive and, up to the very end of the race, leading and in a great position. But then we failed with just three laps to go whilst leading.
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“The racer in me would always rather fail, which happens unfortunately, whilst leading, but I am extremely sorry to Marcus and the valiant MSR team, just heartbreaking and we are extremely sorry for distress caused to Marcus and the team.
“We will investigate and find out what has happened. We push things to the limit, so we are always managing risk with very highly stressed components.
“We will find out what went wrong, learn and come back fighting. We win together and we lose together.”
Reliability has been thrust into the spotlight this year with known engine issues for Chevrolet during the Indianapolis 500 while hybrid-related failures have proven problematic.
Armstrong was classified 24th at Road America. He sits 11th in the standings just behind compatriot Scott Dixon.
IndyCar resumes on July 5-7 at Mid-Ohio.
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