Williams beat the Russian 6-3 6-2 to take the lead over Dinara Safina.
Safina, the previous lead contest holder, fell out from the number one slot after her stunning loss against Zhang Shuai in round two.
Jelena Jankovic was another defending champion to lose in the first round, dropping to Peng Shuai. Other top competitors slowly retired from the ladder early in the competition.
American Williams dominated within the first hour placing three aces and one double-fault over Makarova setting up her rise to world number one.