Once the deal goes through, Glencore will then offload assets to Canadian grains businesses Agrium, which owns Landmark in Australia and Richardson International.
Agrium will acquire a majority of Viterra's agri-products business and Richardson International will acquire a portion of Viterra's Canadian grain handling assets.
It is a neat deal that is likely to mean Glencore is unlikely to run foul of Canadian competition and foreign ownership laws which sunk BHP's bid for Potash Corp.
Glencore is paying a hefty premium for Viterra, with the offer of C$16.25, a 48 per cent premium over Viterra's share price of C$10.98 on March 8 before Viterra informed the market it was the subject of interest from other companies.
The deregulation of both the Canadian and Australian grain markets has led Glencore to the investment.
Glencore's director of agricultural products Chris Mahoney said the company saw strong potential in both Canada and Australia, in particular Australia's proximity to the burgeoning Asian market.
The company said it believed the acquisition would benefit Australian growers by expanding its footprint here and through efficiency gains driven by synergies created through the combining of the Glencore and Viterra businesses.
Glencore's head of Australian grain operations David Mattiske said the transaction "reflects our very strong belief in the potential of the Australian grain industry".
"It will be business as usual for the Viterra operations," Mr Mattiske said.
"We believe the business presents strong growth opportunities and this will be good for growers, employees in the business, and for the industry more generally.
"We will be excellent custodians of these assets. We will be a safe pair of hands, keeping them state of the art and bringing in worldwide best practices.
"We will certainly invest to maintain and expand that infrastructure as necessary.
"We established our agricultural business in Australia nine years ago and we've been well supported here.
"We will now be able to take the next step and extend the benefits of Glencore's global market and logistics capability and its financial strength to more Australian growers."
On the retail side of the Australian industry, Agrium will acquire all Viterra's retail assets which are mainly located in South Australia and Victoria.
It will buy the assets for A$1.73b with the deal also including approximately 90pc of Viterra's Canadian retail facilities as well as its minority position in a nitrogen facility located in Medicine Hat, Alberta.
Richardson International will acquire 23pc of Viterra's Canadian grain handling assets, certain distribution and processing assets in North America for A$768 million.
Meanwhile, Glencore has other takeovers on its mind.
The whopping $34.3b proposed takeover of coals and minerals business Xstrata is still very much on the table.
Analysts have said that while the timing of the Viterra deal is a surprise given the work going on with Xstrata, the direction is to expand into growing markets, with Glencore estimating grain and oilseeds markets to continue growing at 3.5pc per annum across the board.
Following the Glencore bid for Viterra, there was also speculation that Glencore could look to boost its American presence with a move for Gavilon.
But a Gavilon spokesperson in the company's Perth office said other than industry press releases, the WA employees knew "nothing else of Glencore's strategic intentions and very little about the prospective sale of Gavilon".
A Glencore spokesperson also tried to divert attention away from the rumoured acquisition.
"I can't comment on Gavilon because we don't comment on speculation," the spokesperson said.
"But just looking at it practically, Glencore is very focused on the new Canadian deal.
"It's a big deal in Australia in terms of the size of these businesses, so that's where we're focused right now.
"Both here and overseas these businesses will need a lot of bedding down."