Weeks earlier the publication by WikiLeaks of emails hacked from the Democratic National Committee proved damaging to Clinton's campaign.
Obama and his Administration looked at various responses before the election including a retaliatory cyber strike, publishing intelligence about Putin, or crippling economic sanctions. But Obama was concerned he might be perceived as attempting to influence the election in favour of Clinton.
One Obama Administration official told the Post: "I feel like we sort of choked. It is the hardest thing about my entire time in government to defend."
The digital bombs programme involves the NSA, CIA and US Cyber Command and was reportedly a long-term operation with the process of setting it up still under way.
A US official told the Post that the "implants" were being put in computer networks that were "important to the adversary and that would cause them pain and discomfort if they were disrupted".
Agencies would be able to trigger them without Trump's authorisation.
In a statement, Obama's spokesman said his response to the Russian meddling had been "robust ... as is evident by [him] raising this issue directly with President Putin".