The court ruled on Friday that neither the EACC nor other authorities should arrest or charge Prof Ndung'u until the petition was heard.
The governor, who has denied involvement in the case, lodged a High Court petition on Wednesday against the order.
The petition is due to be heard next month.
The High Court has blocked the anti-corruption agency from pursuing claims of abuse of office against the Central Bank of Kenya governor, his lawyer said on Friday, pushing back a decision on a case that could trigger economic ructions.
Director of Public Prosecutions (DPP) Keriako Tobiko this week ordered the Ethics and Anti -Corruption Commission (EACC) to charge governor Njuguna Ndung'u in a case related to the award of a tender to install security software at the bank.
The governor, who has denied involvement in the case, lodged a High Court petition on Wednesday against the order.
The court ruled on Friday that neither the EACC nor other authorities should arrest or charge Prof Ndung'u until the petition was heard, his lawyer Donald Kipkorir told Reuters in a text message.
The petition is due to be heard next month.
If charged, the governor would be suspended from office, creating uncertainty in east Africa's biggest economy at a time when many emerging markets are being buffeted by cuts to US monetary stimulus, although Kenya has so far escaped unscathed.
"We are going to abide with the court order," EACC spokesman Amaro Yassin told Reuters.
In documents submitted to the High Court in Nairobi on Wednesday, Prof Ndung'u said he was not involved in the tender process and that the tender was awarded by an authorised body.
The documents said the Prof Ndung'u was at the time in Paris attending an event in his official capacity.
Prof Ndung'u, who became central bank governor in 2007, weathered a political storm in 2012 after parliament tried to oust him over currency turmoil in 2011, when the shilling weakened sharply and inflation soared.
PAYE Tax Calculator
Note: The results are not exact but very close to the actual.
