The property website firm has announced it will not be seeking to renew its backing of the Barclays Premier League outfit when its current deal expires at the end of the season.
Anelka's 'quenelle' gesture, which he performed after scoring at West Ham on December 28, sparked furore, particularly in his native France, where it has been declared as anti-Semitic and racist.
The action of placing fingers on the opposite shoulder has also been described as a lesser-known Nazi salute.
The Football Association has been investigating the matter and it is understood that they could reach a conclusion this week, probably as early as Tuesday.
With concern about the issue, Zoopla, which is co-owned by Jewish businessman Alex Chesterton, has decided to end its support.
A statement from the company read: "Zoopla has been reviewing its position over the past few weeks in light of the actions of striker, Nicolas Anelka, during the match against West Ham over the Christmas period and has decided to focus its attention on other marketing activities after this season."
The news brings a sour end to a sponsorship deal that had been the biggest and most comprehensive in Albion's history, worth £3million over two years.
It had been reported that Zoopla was unhappy about Anelka's continuing presence in the team while the matter was being investigated.
There were also suggestions the company had asked for Anelka to play in an unbranded shirt if he was to be selected for the Monday night game against Everton.
Neither of these have been confirmed by the company or the club, who are also yet to respond to Zoopla's public statement.
Lawrence Hall, head of communications for Zoopla, said: "Through our sponsorship of West Bromwich Albion we are pleased to have supported the local community and charities.
"In recent weeks, however, we have decided to re-evaluate this sponsorship and as a result we will focus our attention on other marketing activities from the end of the season."
Anelka denied he was being anti-Semitic or racist by celebrating in such a way and claimed he did it in support of his friend Dieudonne M'Bala M'Bala, a controversial anti-establishment comedian.
The 34-year-old did promise not to repeat the gesture.
Since beginning its investigation, the FA has made no comment other than to state an independent expert has been used during the probe.
Anelka could face a ban if deemed to be guilty of breaching their anti-racism rules.