Keothavong had managed a confidence-boosting three set win over world number 41 Jarmila Groth the day before, but couldn't repeat her efforts on Wednesday.
Serena had made hard work of beating another Russian, Vera Dushevina, in a three-set opener on Monday, but appeared in command against world number 18 Petrova as she won the first set.
Amla was unfortunate to be given out - Daryl Harper rose his finger despite Pattinson's delivery looking set to miss leg stump - but the number three was delighted with how day two turned out for South Africa.
Eleventh seed Gonzalez of Chile and number three seed Nadal of Spain were in their 2nd straight tie-breaking set, with Nadal leading 7-6 (7-4), 6-6 (3-2) when play was suspended.