Jewish community leaders said they were disturbed by parallels they saw between the red-tinged drawing and historical anti-Semitic propaganda.
The Board of Deputies of British Jews said it had lodged a complaint with the Press Complaints Commission.
The deputies said in a statement that the depiction of a Jewish leader using blood for mortar "is shockingly reminiscent of the blood libel imagery more usually found in parts of the virulently anti-Semitic Arab press".
In a statement, the paper's acting editor Martin Ivens said that insulting the memory of Holocaust victims or invoking blood libel was "the last thing I or anyone connected with the Sunday Times would countenance".
"The paper has long written strongly in defence of Israel and its security concerns, as have I as a columnist," he said.