A third politician is also considering leaving the party, according to the Moderate's Stockholm chairman Sten Nordin.
Councillors Petter Lindfors and Rolf Könberg announced their decisions to leave their posts prior to the presentation of the results of an external party investigation.
Mats G Nilsson, a member of parliament, is also considering his future in the party, Nordin told reporters on Friday morning.
A handful of Stockholm Moderates have been identified as having paid memberships for new recruits to the party who have pledged to vote for them.
Accountancy firm Ernst & Young was hired in by the party to examine whether more new party members had their fees paid by an existing member.
The firm presented its report on Friday after having contacted 146 new members and checked to see if their memberships had been paid by someone else, which is not permitted according to party regulations.
The probe was launched following revelations that Mats Rudin had paid the membership fees of "a number of" new members to boost his own run for parliament.
Rudin, who was eighth on the party list for the autumn parliamentary election, had already conceded his place.
Reporters were told on Friday that Rudin had left address and identification details of the new members, as well as their 100 kronor fees, to three other Moderate candidates who then registered their memberships.
Petter Lindfors and Rolf Könberg denied in personal statements that they had broken any regulations. Despite their denials they explained that they are leaving politics as the price had become too high.
"Family is more important that my political position," Petter Lindfors wrote.
"Life is much bigger than politics," Rolf Könberg said.
At the press conference, Sten Nordin said that the pair "had not lived up to the spirit of the regulations."
"I am both sad, angry and disappointed after what is perhaps the worst week that my political association, Stockholm, has experienced," Sten Nordin, Stockholm mayor and local party chairman, told reporters.