Tussles broke out at the Western Wall on Nov. 2, during the first of a series of events planned by liberal Jewish groups for a day in protest of ongoing restrictions on non-Orthodox worship at the foot of Judaism's holiest site.
Video footage appeared to show at least 100 people joining the march and prayer service. The Times of Israel reported.
The Israeli Reform movement said in a press release that "dozens" of Torah scrolls were carried into the women's section.
Security guards from the Western Wall Heritage Foundation tried to forcibly prevent the protest prayer group of some 200 people from entering the main site with the Torah scrolls, but were unable to hold back the momentum of the crowd, the Jerusalem Post reported.
The demonstration had been called over the failure of the Israeli government to provide a promised egalitarian prayer space at the Western Wall, which was agreed in January after three years of negotiations.
Before Wednesday's protest the Israeli prime minister, Benjamin Netanyahu, accused by protesters of reneging on a commitment to regularize a liberalized prayer space, called on Jews living outside Israel to show "patience and tolerance" over the issue, The Guardian reported.
"We have one people and one wall – it's our wall," he said. "The less publicly we talk about it, the better chance we have to resolve it. The last thing we need is more friction, as that will make a solution more difficult."
The prayer and protest came at the start of the new month on the Hebrew calendar, a day after Netanyahu urged liberal Jewish movements to refrain from voicing protest over the enduring status quo on worship at the Western Wall.
Social media video showed scuffles as some ultra-Orthodox onlookers and Western Wall officials lunged for the Torah scrolls carried by the protesters and attempted to physically bar them from entering the prayer area.
Anat Hoffman, chair of Women of the Wall, a group campaigning for pluralistic prayer services at the holy site, was elated at her group's success at holding its morning prayers at the Wall, said The Ttimes of Israel.
"I feel this day is Simhat Torah, a little late," she told Israel Radio. Simhat Torah is a holiday that celebrates the completion of the annual cycle of Torah readings. It fell on October 24 this year.
"For the first time in history," Hoffman added, "a Torah scroll is in the women's section. It's a historic day. Every day, women should be allowed to read from the Torah if they're interested. And at bat mitzvot. The time has come."
While segregation of the sexes during prayer is long established within the Orthodox tradition, Conservative, Reform and other liberal forms of Judaism allow men and women to pray together.
Members of the Women of the Wall carry a Torah scroll after prayers in the women's section of the Western Wall.