An internal inquiry found 30 teams worked for more than two years to try to ensure a conservative candidate won.
Park Geun-hye did beat liberal Moon Jae-in, but she is now facing trial for corruption and abuse of power and Mr Moon has replaced her.
Former spy chief Won Sei-hoon is currently on trial for a second time for trying to manipulate the election.
He was sentenced to three years in jail in 2015. The conviction was overturned on appeal and the new trial was ordered.
The in-house investigators at the National Intelligence Service (NIS) said the agency had hired internet experts to try to sway public opinion through social media postings.
The operation was intended to ensure that outgoing President Lee Myung-bak was succeeded by another conservative.
Ms Park won by a narrow margin.
"The teams were charged with spreading pro-government opinions and suppressing anti-government views, branding them as attempts by pro-North Korean forces' to disturb state affairs," the investigating team said.
It also found that the NIS had tried to influence parliamentary elections in 2011 and 2012, as well as placing some opposition politicians under surveillance.
The new president has vowed to reform the NIS, and the new spy agency chief has pledged to end any involvement in domestic politics.
However, a spokesman for Ms Park's party said the inquiry itself showed the NIS continued to interfere.
The spokesman, Kang Hyo-sang, said: "The NIS says it will dissociate itself from politics but it is meddling in politics again by starting this probe."
Ms Park was charged in April with bribery, coercion, abuse of power and leaking state secrets.
She is accused of allowing close friend Choi Soon-sil to extort money from companies in return for political favours. She denies the charges.

Trouble is, the aspen tree itself doesn't like to produce seeds which makes life very difficult for everyone.
But last year I visited Shropshire company Forestart and helped them out with their plans to get their aspens in a seed producing mood.
Forestart harvests a billion wild tree seeds every year to grow into new trees for planting.
You can read a blogpost about their plans here, but here's the general gist.
Aspen trees usually reproduce by sending up suckers, thin plants that are clones of the parent tree.
That's no good for Forestart who need seeds to grow new aspens.
The last time aspens in Scotland flowered and produced seeds was twenty years ago.
So Robert Lee from Forestart had a plan. I helped him remove a ring of bark around each of his aspen trees.
Not all the way around as that would kill the tree, but a strip about an inch wide round most of the trunk.
The idea was to simulate a beaver attack on the tree, stressing the tree out and forcing it to produce flowers and then seeds.
Well this week I returned to see if the experiment had worked and an amazing sight greeted me, eight aspen trees all covered in catkins. It's something that you very rarely see in nature.
Robert explained to me I'd missed the very best display and a windy day had rather done for the flowers on the male trees but overall it was a remarkable thing to see.
It's also really good news for Robert as if all goes to plan he and his team will be able to gather a huge volume of aspen seeds later in the year.
Can we be sure it was our intervention that made the difference?
Well yes, as Robert cut the bark so that some trees had branches below the exposed part of the tree.
Those branches had no flowers, no catkins, while the rest of the tree was laden.
It's not totally clear why this worked, it could be the stress as Robert first though or it might be the ring of removed bark blocks the goodness in the aspen leaves from returning to the roots and instead keeps it all in the tree canopy which in turn leads to an eruption of flowers.
The trees themselves are healing nicely and while this won't be an annual event it is something Forestart could repeat in the future.
Meaning more chances for people who want to plant this most wonderful of our native trees.
The only slight cloud on the horizon is if the whole effort is too successful, we get a lot of seeds and the local bird population treat the aspen seeds as a very expensive lunch.
Fingers crossed the siskins find something else to eat instead!
South Korea's spy agency has admitted it tried to manipulate the result of the 2012 presidential election.
[NEXT_CONCEPT]
Aspens are one of our most beautiful native trees and there's a huge demand for seeds to grow new ones for planting.