Berkshire portfolio managers Todd Combs and Ted Weschler, who each invest about $9 billion, made the investments.
Berkshire's new stake in Apple totaled 9.8 million shares, while the company boosted its shares of IBM by 198,853 to 81.2 million shares. Shares of Apple were up 4 percent in afternoon trading. (Get the latest quote here.)
"I think this is basically an example of how there's a transition going on in Berkshire Hathaway," Vahan Janjigian, chief investment officer of Greenwich Wealth Management, said on CNBC's "Power Lunch" on Monday.
"For years, this company has been run by Buffett and [Charlie] Munger. ... What's going on especially with the Apple investment today is that Weschler and Combs are taking over the investment decision-making process."
Berkshire's investment in Apple puts it at odds with investors that have retrenched from Apple.
Last month, billionaire activist investor Carl Icahn said he sold his entire Apple stake, on concern that China could make it harder for the company to do business there.
While the seeming divergence between Berkshire and several major investors could be seen as a worrying sign for some, Janjigian said he's not concerned.
"It's also notable to look at what tech companies they aren't investing in," he said. "They bought IBM and Apple but they haven't bought Amazon and Tesla, which tells me that they're still very value-driven.
Berkshire also boosted its holdings in Visa by 3.6 percent to 10.2 million Class A shares, increased its stake in Phillips 66 by 22.9 percent to 75.6 million shares, and upped its stake in Bank of New York Mellon by 3.6 percent to 20.8 million shares.
Berkshire reduced its holdings in a number of big names, as well. It lowered its holdings in Wal-Mart Stores by 949,430 to 55.2 million shares, and dissolved its stake in AT&T, according to the 13F filing.
The changes in the company's holdings are as of March 31, 2016 and compared with the previous quarter ended as of December 31, 2015.
— Reuters and CNBC's Akane Otani contributed to this report.