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.
Miller said, "The market's got this right" in terms of how it viewed the Amazon-Whole Foods deal.
"The market thinks that is a good deal. It's going to be value-accretive," he said. "It indicates that Amazon is serious about the grocery business. This means they're in it for the long haul."
MIller earned his reputation for decades of strong performance as the only active manager to beat the market 15 years in a row, between 1991 and 2005. His performance went south during the financial crisis, and he left his longtime firm Legg Mason and struck out on his own a few years ago.
While still well-regarded in the industry, Miller has his critics as well. Morningstar gives the Opportunity Fund just a two-star rating, with analysts saying Miller is too fond of risk without hedges in his portfolio.
Valeant has come under fire for pricing practices on its prescription drugs and is down 12.8 percent year to date and more than 95 percent from its July 2015 peak. However, Miller remains a believer.
He praised new CEO Joe Papa and predicted the stock would rise 50 percent over the next year and hit as high as $60 in the next three to five years. Valeant closed Friday at $12.66.
Finally, Miller and his son, Bill Miller IV, are also big bulls, believing the digital currency whose price has soared this year is bound for disruptor status.
"It is a true disruptor and true innovation in money," the elder Miller said. "We haven't seen that in thousands of years."