Home favourite Protasov clocked a time of 18:46.04 on the 28.95km test in an M-Sport Ford Fiesta RRC.
Pajunen lost more than 20s to Protasov on the stage and now drops 14.2s behind the Ukrainian driver in the overall classifications.
Third fastest was Fiesta S2000 driver Yagiz Avci, completing the stage 19.1s behind Pajunen.
Valeriy Gorban, at the wheel of a Ralliart Mitsubishi Lancer Evolution IX, was fourth fastest and quickest out of the IRC Production Cup competitors.
Despite reporting problems with the brakes on his Subaru Impreza R4 STI on the previous stage, Marco Tempestini set the fifth fastest time.
Yuriy Kochmar’s lead in the IRC Production Cup has been slashed to a mere 0.3s following Tempestini’s impressive stage time.