El-Toukhy was the only woman directing a feature film in the main, 21-strong movie line-up, a disparity that drew criticism during the festival and prompted renewed scrutiny of the barriers facing women in cinema.
Set in the aftermath of World War Two, Woman Unknown follows a housemaid played by Arcel whose past relationship with a German soldier threatens to destroy her future.
The film unfolds against the backdrop of a newly liberated Denmark, where women accused of fraternising with occupying German forces were often subjected to vigilante justice.
"To me personally, Woman Unknown is about the female body as a battleground and a public matter. And at the same time, the film tells the tale of women who are invisible, unseen, and voiceless," el-Toukhy said in her acceptance speech.
South Korean director Lee Chang-dong took the runner-up Silver Lion award for Promised Love, while Russian-born filmmaker Ilya Khrzhanovsky won best director for DAU, a hugely ambitious project shot largely in Ukraine before the ongoing war that has attracted intense scrutiny and controversy.
Khrzhanovsky, who has renounced his Russian citizenship and is a fierce critic of Moscow, dedicated his prize to Ukraine.
John Malkovich won the best actor award for his role as an ageing, maverick CIA agent in Martin McDonagh's razor-sharp comedy Wild Horse Nine.
The Venice festival marks the start of the awards season and regularly throws up big favourites for the Oscars.
However, many of the big studio-backed contenders that once crowded the Venice schedule were absent this year as Hollywood reconsiders how to market its movies and cut costs.
In a change of tone, the festival offered a program steeped in global politics and social upheaval, including NAZA - a hard-hitting documentary by Israeli directors Yuval Abraham and Rachel Szor that won the Special Jury Prize.
Based on anonymous interviews with 24 Israeli intelligence officers and soldiers, the film accuses the Israeli military of routinely approving mass civilian deaths when they target militants in the Gaza Strip.
Israel has denied the charge.
The documentary received a record 25-minute standing ovation at its premiere on Thursday - the second year in succession that a film about Gaza has resonated in Venice after The Voice of Hind Rajab, a true-life account of the killing of a Palestinian girl during the war.
"The Israeli intelligence officers we spoke with talked to us about how this mass killing is systemic, not by accident, but by design," Abraham said on Saturday.
"We believe that the denial of a crime is what helps it persist."
Stephane Brize, Coralie Amedeo and Olivier Gorce received the screenplay award for their well-received French workplace drama A Good Little Soldier, while Malou Khebizi was named as best emerging young actor for her role in another well-received French production - A Place To Heal.
Festival director Alberto Barbera has defended the male-dominated line-up this year, insisting that selection decisions were based on artistic merit rather than quotas, and urging the industry to do more to help women break into the business.
El-Toukhy said women filmmakers continued to face greater difficulties securing financing, limiting budgets, casting opportunities and ultimately access to major festivals.
The head of the main jury, US actor/director Maggie Gyllenhaal, also weighed in, telling reporters that female filmmakers often struggled to secure financing because the stories they want to tell were not seen as important.
