A major shareholder in the online retailer himself, Miller said Amazon CEO Jeff Bezos has moved on a company that fits in well with his overall investing strategy.
"Jeff is one of the world's great capital allocators," Miller said during a live interview on CNBC's "Closing Bell." "What this means is he knows, he's highly confident they can earn way above the cost of capital on this one."
In a deal valued at $13.7 billion, or $42 a share, the move takes Amazon from the king of online sales further into the world of brick-and-mortar retail establishments. Investors saw the move as a positive, sending Amazon shares up 2.4 percent to $987.71 in Friday trading, while boosting Whole Foods' price 29 percent to $42.68.
Amazon is the fourth-biggest holding in Miller's $1.4 billion Miller Opportunity Fund, which has easily outdistanced most of its peers this year with a 12.7 percent return, putting it in the third percentile of Morningstar-rated funds in its category.