Davis had finished last on stage 2, 149km between Airolo and Crans-Montana , the Australian nearly 24 minutes behind winner Juan Mauricio Soler (Movistar).
He told news agency AFP: "I just woke up feeling crook.
"Yesterday (Sunday) I felt it coming on and by the time I got to the start of the stage it was clear I couldn't race."
Davis was deflated after coming off what he describes as "Great form to my worst form ever in 1 week!" The former Australian champion's last race was at the Tour of Belgium where he recorded a string of top 10 results.
It's been a difficult few months for Davis, who in May, claimed he was being shunned by Astana management at the Tour of Turkey over interest in Shayne Bannan's GreenEdge project which could join the WorldTour in 2012.
Davis' participation in next month's Tour de France seems unlikely with Astana appearing to favour Kazakhstani riders for the big races. He hasn't started in the Tour de France since 2005 when he was riding for Liberty Seguros - Würth and he came fifth in the points classification.