Legal representative Willie Spies said the civil rights group launched a court application in October 2012 on behalf of Gordon Thomson, one of numerous pensioners who had received a two percent pension increase the last 11 years.
Thomson had applied to the court to force Transnet and the Treasury to come up with an interim solution to help him and other pensioners, mediated by Parliament's public enterprises portfolio committee.
He was a member of Transnet's second defined pension fund.
In its reply to Thomson's application, Transnet argued that the transport pension fund should be added as a party before the case could resume.
Both pension funds opposed the interim court application, heard by the High Court in Pretoria last week.
Spies said Judge Selby Baqwa ruled in favour of Thomson and ordered that the transport pension fund be joined as a party.
"He ordered Mr Thomson to supplement his application in preparation for the case against the second defined pension fund and the transport pension fund."
Spies said the "table has now been set" for the conclusion of the application before the end of the year.
The application ran parallel to a separate class action launched by another group of Transnet pensioners.
In this civil claim, about 66,000 pensioners wished to recover about R79 billion, which they claim Transnet took from their pension funds.
The funds' most important assets, acknowledgements of debt worth R7.7bn which generated an annual income of R1.2bn, were apparently "swapped" in early 2001 for MTN shares, known as M-Cell at the time, worth about R1.4bn.
Leon Kellerman SC, for the pensioners, wrote in court papers: "There is no indication that the funds received any income from the M-Cell shares."
About 80 of these pensioners marched peacefully to the Union Buildings in Pretoria last month to hand a petition to President Jacob Zuma's office. They had asked for his urgent intervention in their fight for decent pensions.
Freedom Front Plus MP Anton Alberts told the marchers that they believed funds had been stripped over a period of more than 20 years.
"That's been found by the investigation by the legal team using an actuary... that multiplies to a claim of almost R80bn. That is the funds lost plus the interest," Alberts said at the time.
Spies said the parties would keep in contact to ensure both applications would achieve the best outcome for the Transnet pensioners.