The summary dismissals are in line with the recommendation of the independent chairman of the disciplinary hearing at which the two managers appeared, Transnet said.
The two were dismissed for manipulating the tendering for security services. They were suspended in November.
Transnet spokesman John Dludlu would not disclose the names of the two senior managers, but said suspended freight rail chief executive Siyabonga Gama was not involved.
Dludlu confirmed that the dismissals related to the GNS Security contract, which has been under investigation.
General Nyanda Security Risk Advisory Services is owned by communications minister Siphiwe Nyanda and was paid R55-million by Transnet under a contract awarded by Gama.
A tender was allegedly awarded to GNS without proper processes being followed.
Public Enterprises Minister Barbara Hogan said in December that Gama was not authorised to sign off on tenders worth more than R10-million.
She said GNS continued to benefit from the contract for several months after Nyanda was included in President Jacob Zuma's Cabinet.
Gama was the front-runner to take over as Transnet group chief executive from Maria Ramos, who quit to join Absa. Gama had the backing of the ANC, the SACP, the ANC Youth League and senior management.
But his suspension scuppered his bid for the top job at Transnet.
Transnet said yesterday that the contract for which the two senior managers were dismissed was awarded in a confined process - meaning without an open tendering or other qualifying bidders being invited to tender - and without following the required governance processes.
It said it was committed to upholding the highest standards of corporate ethics and governance.
"Employees are expected to comply with all company policies and procedures and act in accordance with the company's values," the company said.
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