The 24-year-old Brit had climbed into second overall, 33 seconds behind race leader Nairo Quintana (Movistar), with a third-place finish on the stage 4 ascent to Terminillo.
"We've still got a couple of days to try something and see what happens. Quintana is looking pretty strong but you never know," Yates had noted after the finish Saturday.
Despite saying that he was "feeling good" after the queen stage, he climbed off Sunday with 75 kilometres left to race on a challenging stage 5 with an apparent illness.
Yates' abandon pushes Quintana's GC lead to 56 seconds over the nearest competitor, Thibaut Pinot (FDJ), who now sits second overall.