As well as the USD 256 million investment, VW's Truck and Bus division will also launch a "strategic technology and supply chain co-operation" and a purchasing joint venture with the US firm, the group said in a statement.
VW commercial vehicles chief Andreas Renschler hailed the move as a "major milestone on our way to create a global champion".
The deal will also see VW Truck and Bus, which unites VW's own-brand heavy vehicles as well as Scania and MAN, take two seats on Navistar's board.
German rival Daimler currently dominates the US truck and bus market with its Freightliner brand.
But Volkswagen is hunting new opportunities as the effects of its drawn-out diesel emissions scandal linger in the minds of ordinary American consumers, weighing on car sales.
The deal was a "first step to improve the footprint of VW Truck and Bus in the US," analysts at DZ Bank wrote, but "we assess the commercial vehicles business to be less important than VW's car business."
Illinois-based Navistar itself in March paid a USD 7.5-million fine to the US Securities and Exchange Commission regulator after having lied about its engines' conformity with emissions rules in the early 2010s.
In its own statement, Navistar said that the VW deal would create at least USD 500 million of synergies over the coming five years.
The US manufacturer has been in business since 1902 and builds trucks, coaches, construction equipment and engines for heavy vehicles, including military ones.
There was better news for the US firm today, with shares leaping 60.13 percent to USD 22.53 by 1355 GMT, shortly after trading began in New York.
Volkswagen shares enjoyed a one-percent bounce in afternoon trading in Frankfurt to 126.10 euros.
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