Watson began well and the two were difficult to separate for over an hour until the British number three surrendered a 3-0 advantage in the tie-break to lose 7-5 and concede the opening set.
And the seventh seed took charge from there, winning six games straight to advance to the quarter-finals.
"The court is beautiful, the public was full so it was very nice," said Czech player Safarova.
"I played very well today but I take it step by step and I will try to do well here."
Eighteen-year-old Robson's defeat later in the day meant no British players remained in the bracket. Former champion Makarova of Russia claimed the opening set over 10 games before clinching game 12 of the second to avoid a tie-break and seal a straight sets win.
The German world number nine bounced back from her scrappy win over Elena Vesnina in the first round with a more assertive performance in a break-ridden last-16 contest.
Tsvetana Pironkova also required three sets to advance, the Bulgarian coming out on top over Stephanie Dubois 6-0 4-6 6-4.
Klara Zakopalova won an all-Czech encounter against Petra Cetkovska, 6-1 1-6 6-2 and in the last match of the day, Austria's Tamira Paszek overcame Daniela Hantuchova of Slovakia 6-4 3-6 6-1.