The Google parent's market cap was about $498.56 billion, compared with $496.69 billion for Apple.
Shares of Apple hit a fresh 52-week intraday low of $89.89 in the session as they dipped below $90 per share for the first time since June 2014.
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Alphabet previously topped Apple as the largest company on Feb. 2 of this year, but the Cupertino, California-based iPhone maker reclaimed its title during the following session.
Apple had been the largest company, after surging past Exxon Mobil in 2012. The two battled for the No. 1 spot in 2013, but since then Apple has been far and away the largest company.
— CNBC's Gina Francolla and Christopher Hayes and contributed to this report.