Zaffir Hakim, 49, was awarded £16,680 after speaking out about discrimination and subsequently losing his job in 2015.
Grahame Smith, who sits on the First Minister’s advisory council on Europe and other public bodies, made the key decisions that led to Mr Hakim’s dismissal.
Mr Smith, general secretary of the Scottish Trades Union Congress (STUC), was branded “not credible” by the judges who heard the case of Mr Hakim.
However, four years on an employment tribunal awarded has awarded him £12,880 for financial loss and £3,800 for injured feelings.
Mr Hakim, 49, who is of Pakistani descent, worked for the STUC for 11 years as a development officer on its anti-racism project One Workplace Equal Rights (OWER).
In May 2014 he raised a claim of race discrimination against the STUC that led to “tension” in the workplace and “soured” his relationship with Mr Smith.
A tribunal later said Mr Smith was worried the claim would make it harder for the STUC to secure public funding for tackling discrimination.
Although Mr Hakim withdrew his claim in December 2014, the relationship remained poor and he was made redundant in March 2015 when funding for his post ended.
Mr Hakim then raised an unfair dismissal action, claiming he had been discriminated against because of his race and victimised.
A tribunal agreed he had been unfairly dismissed and victimised, but not because of his race.
Mr Hakim said he was pleased the tribunal was at an end, but disappointed with his award.
He said: “I don’t think it’s reflective of how I was treated.
“The case has gone on for so long too and it’s been really stressful, impacting on my health, so I’m a bit disappointed with the outcome.
“I just hope the STUC act on the recommendation and start to practise what they preach to ensure this never happens to another worker.
“The STUC of all organisations can be culpable of such action, it should be a wake-up call for all organisations to review their policies and procedures and their treatment of their black minority ethnic staff.”
Employment judge Claire McManus criticised the STUC for failing to follow correct redundancy procedures by not considering Mr Hakim for other vacancies.
Her findings also found the STUC failed to hold proper meetings or keep notes.
She described Mr Smith’s evidence in the case as “not credible” on a number of points, including his description of how he made the key decision.
The tribunal recommended the trade union umbrella body should review its redundancy procedures.
A spokesman for the STUC said: “The judgement confirms that we were faced with a genuine redundancy situation.
“We have fully accepted that our processes and procedures were insufficiently robust to deem the redundancy fair.
“We have already completely reviewed and amended our processes and procedures to ensure that this will never happen again.
“The award is significantly less than what was claimed and the judgement also makes clear that Mr Hakim contributed to his own dismissal and our failings, while deeply regrettable, were largely procedural.”