Woods, whose career has been hampered by multiple injury setbacks and dealt with back spasms in Thursday's first round, withdrew after hitting his tee shot at the seventh hole and at one point while being carted back to the clubhouse buried his face in his hands.
"I would like to confirm that I had to withdraw from @thegenesisinv due to illness, which we now know is influenza," the 15-times major winner wrote on social media on Saturday. "I am resting and feeling better.
"Good luck to the players this weekend. I'm disappointed to not be there and want to thank @GenesisUSA and all the fans for the support."
Woods' longtime business partner Rob McNamara told reporters on Friday that Woods woke up that day with a fever, was feeling dizzy during the round and after withdrawing received treatment, including intravenous fluids.
When Woods, 48, returned to the clubhouse he was not seen for about two hours and the sudden arrival of an ambulance and two fire trucks sparked concern, though it was later reported that they were there to deliver IV fluid bags.
Woods eventually emerged and walked out of the clubhouse and into the passenger seat of a courtesy car.
There was plenty of excitement ahead of this week's event as it marked the first PGA Tour start for Woods since last April's Masters, where he withdrew before completing the third round because of plantar fasciitis.
Woods had ankle surgery later that month and spent most of the rest of the year recovering.
Woods returned to professional golf at the end of November in an unofficial PGA Tour event – the Hero World Challenge – and at the time said he intended to play one PGA Tour event a month this season.
