The presented work describes the development and validation of a rapid UHPLC-UV method using a core-shell particle column with a pentafluorophenyl stationary phase for the separation and quantitative analysis of the six anthocyanins in acai berry and dry blueberry extracts. The anthocyanins (cyanidin-3-glucoside, cyanidin-3-rutenoside, delphinidin-3-galactoside, delphinidin-3-glucoside, delphinidin-3-rutenoside, and peonidin-3-glucoside) were separated and analyzed in 5 min. The chromatographic separation was performed on a Kinetex PFP (150 × 2.1 mm) core-shell column with a particle size of 1.7 μm at a temperature of 50 °C. Acetonitrile was used as mobile phase B and 5% formic acid, filtrated through a 0.22 μm filter, as mobile phase A. They were delivered at a flow rate of 0.55 mL min−1 according to the elution gradient program. The detection wavelength was set at 520 nm. A solid-liquid extraction with a solution of methanol and a 5% water solution of formic acid (25 + 75 v/v) using an ultrasonic bath was chosen for the preparation of the available commercial samples of food supplements with a content of acai berry extract and blueberry extract. Under optimal chromatographic conditions, the method was validated. Recoveries for all analyzed anthocyanins were 97.8–102.6% and the relative standard deviation ranged from 0.4% to 3.0% for within-day and from 0.6% to 3.1% for between-day repeatability. The limits of detection were in the range of 0.11–0.14 μg mL−1.