The Western Wall, one of the holiest sites in Judaism, is governed by the ultra-Orthodox Jewish establishment and women and men must visit it separately.
The rule was applied to journalists gathering to cover Pence's visit, effectively forcing women to stand behind men, leaving them with worse access.
A podium erected for journalists to cover the visit included a barrier between the male and female sides of the wall, with women journalists forced to stand behind it.
After complaints, a tarp covering the podium was removed, allowing women to stand on chairs to be able to see over male journalists.
Some women journalists at the site were posting on Twitter about the separation, using the hashtag #PenceFence.
"I feel like a second-class citizen," Tal Schneider, a journalist with Israeli paper Globes, told AFP. "We are not allowed to do our work."
Schneider said she was told by US officials that the arrangement was at the insistence of ultra-Orthodox Jewish authorities at the site.
"Every effort was made to accommodate both female and male journalists while observing the rules in place at the Western Wall," Pence spokeswoman Alyssa Farrah said later.
The holy site has long seen controversy over the separation between women and men.
Reformist Jewish movements have sought to change the rule, but the ultra-Orthodox authorities have firmly refused, citing Jewish law.
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