Andretti Autosport will switch from Chevrolet to Honda power from the 2014 IndyCar season in what the team says is a multi-year deal.
The news comes as little surprise in light of Ganassi's recent defection from Honda to Chevrolet.
With GM also being aligned with Penske, a move by Andretti in the other direction would save it from having to fight with two other marquee teams for one manufacturer's attention, while also ensuring that Honda continues to supply a team with recent championship-winning credentials.
"It's sort of like going back to family," said team boss Michael Andretti.
"This team, back to when it was Team Green, was one of the Honda factory teams in the mid-1990s.
"We feel like we're going back to great people. Chevrolet was great to work with and we had great success with them, but we felt that Honda was the best option for us going forward and we're very excited about it."
HPD president Art St Cyr said that a team of Andretti's pedigree was vital to Honda's hopes of winning drivers' and manufacturers' titles.
"Clearly, the Andretti team has been very strong over the last couple of years," he said.
"Our ultimate goal is to win championships, so it is important to have strong driver line-ups that work together and raise everybody's game so that we have a chance to win every single weekend."