Albert Scardino has decided not to renew his contract in order to pursue other interests, the paper said. Sources denied that his departure was connected to the dismissal of Aslam.
The trainee journalist, 27, was sacked for refusing to leave Hizb ut-Tahrir, an extremist Muslim political group which has been criticised for anti-semitism. Although it is legal in this country, it is proscribed in Germany and elsewhere.
The paper found itself under attack after it published a comment piece by Mr Aslam on the 7 July attacks on London which did not make Mr Aslam's political affiliations clear.
Mr Alsam did not inform The Guardian of his membership in his application. But sources said in the newsroom he made no secret of his membership.
Mr Aslam was given the opportunity to leave Hizb ut-Tahrir. He declined to do so, and was sacked.
Sources at The Guardian claimed that Mr Scardino was among the senior editors who were aware of Mr Aslam's membership.
A Guardian spokeswoman said: "He has decided not to renew his contract. I don't think it has anything to do with Dilpazier Aslam."
Mr Scardino, whose wife, Marjorie, is chief executive of the Pearson group, which owns the Financial Times, was yesterday unavailable for comment.