Apple had held the lead since Q3 2014.
Lenovo shipped just under 16 million PCs, some 240,000 more than Apple.
The PC market fell 12 percent annually to 109.2 million units, with double-digit percentage declines affecting desktop, notebook and tablet shipments.
Apple, HP and Dell followed Lenovo, with marginal increases in their shares of the declining market.
Samsung, which is in the top five, experienced a slight dip in share due to slowing tablet sales and the scaling back of its notebook business.
The PC market report said Apple and Lenovo lead the market in their home countries of the US and China respectively. But Apple is heavily reliant on worldwide iPad shipments, which totaled 10.9 million units this quarter.
Apple iPads represented 70 percent of Apple’s total PC shipments in Q2.
Tim Coulling, Canalys Senior Analyst said: “With a more diverse product portfolio, Lenovo is in a stronger position than Apple to cement its lead in the market. But it is not without its own challenges, and has recently had to take steps to clear a significant build-up of PC inventory in EMEA.”
Lenovo controls almost 30 percent of the Chinese PC market and is steadily building its share in the US.