Spain’s world number five Ferrer, given a bye into the second round, used his superior retrieving game to dominate the Russian despite only getting half his first serves in.
Ferrer broke his opponent four times on his way to victory and will face Igor Sijsling after the Dutch world number 97 surprised Spain’s fifth seed Feliciano Lopez 7-6(0) 7-6(2).
Fourth seed Alexandr Dolgopolov also went out, the Ukrainian losing 6-3 3-6 6-3 to Colombia’s world number 61 Alejandro Falla.
Falla faces France’s Julien Benneteau in the quarter-finals.
Second seed Juan Monaco did reach the quarter-finals though, with a 6-4 7-5 victory over Jimmy Wang.
Monaco did not overwhelm the wildcard, suffering three breaks of serve across the two sets, but still did enough to progress in Kuala Lumpur.
The Argentine plays Canada's Vasek Pospisil in the last eight as he goes in search of his fourth title of the year.
Russia's Nikolay Davydenko also reached the quarter-finals with a 7-5 6-4 win over Denis Istomin.
The former world number three is looking to improve on a semi-final in Metz and will play third seed Kei Nishikori after the highly-rated young Japanese bounced back from dropping the first set to beat Albert Ramos 6-7(5) 6-2 6-1.