Williams, a five-time Wimbledon champion, was a surprise choice to play on one of the All England Club's smaller outside courts for her 7-5, 4-6, 6-3 over Greek qualifier Maria Sakkari.
Former Wimbledon champion Martina Navratilova tweeted "it stinks" when she learnt of the scheduling move.
Venus, 36, was followed on to the court by Australian Open champion and fourth seed Angelique Kerber, while on Centre Court, Japan's Kei Nishikori faced France's Julien Benneteau in a match between two players without a Major title.
In contrast, Venus has seven Major titles to her credit and, while she said she had no qualms about playing on any court, she made it clear she felt the Wimbledon chiefs, who were the last of the four Grand Slams to agree to equal prize money, were prioritising men over women.
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"It's not the ideal schedule for the women. We'd like to see equal amount of matches. We don't want more, just the same amount, that's all," she said.
"I played many times on outside courts. It didn't matter how many titles I had won or what my ranking was at that time. It didn't make a difference whether I played on an outside court or a centre court.
Venus hadn't lost to a player outside the top 100 at a Grand Slam since a 1999 defeat against Barbara Schwartz at the US Open.
But the 36-year-old, the oldest woman in this year's main draw, was teetering on the brink of an embarrassing second round exit when world number 115 Sakkari levelled at one-set all.
Williams held her nerve to subdue Sakkari in two hours and 24 minutes and will play Russian 29th seed Darya Kasatkina for a place in the last 16.
She now has 78 Wimbledon match victories, second among active players behind her sister Serena Williams' tally of 80.