Mr Johnson’s wife, Carrie, will also not receive a second fine.
They were both issued with £50 Fixed Penalty Notices last month for breaking Covid laws at a birthday party for Mr Johnson in Downing Street in June 2020.
The Metropolitan Police said the inquiry into lockdown breaches in and around Downing Street had now ended.
It issued a total of 126 fines to 83 people, for events happening across eight different dates.
It had been widely expected that Mr Johnson, who reportedly attended up to six of the gatherings investigated, would be fined again.
Police examined 510 photographs, as well as CCTV images, emails, logs of entries into buildings, diary entries and witness statements.
They also studied 204 questionnaires from people who had attended events.
Following the investigation, the UK’s top civil servant, Cabinet Secretary Simon Case, has been told he will not be fined, sources have told the BBC.
In December, he was forced to step aside from his role leading an inquiry into lockdown parties, after it emerged an event had been held in his own office.
The ending of the police investigation paves the way for the publication of the full report by senior civil servant Sue Gray, who took over the inquiry into lockdown gatherings from Mr Case. This is expected to happen next week.
An interim version of Ms Gray’s report, published in January, criticised “failures of leadership and judgement” in No 10 and the Cabinet Office.
Some Conservative MPs have previously said they are reserving judgement on Mr Johnson’s future until the final document is published.
The BBC is aware of about 20 who have called for a vote of confidence in Mr Johnson’s leadership over the Partygate revelations.
Mr Johnson also still faces investigation by a Commons committee over claims he misled Parliament about parties during lockdown.
Some are wondering how Boris Johnson managed not to accumulate one or two more fines.
But we now know that isn’t going to happen. The Metropolitan Police’s role in all this is done.
You might be reading this boiling with anger about what went on. Or perhaps you are past caring, or never really cared at all.
But this mattered: morally to some, legally to others and politically to plenty, and it still does.
Labour leader Sir Keir Starmer said the number of fines showed there had been “industrial-scale lawbreaking in Downing Street”.
He added that his opinion of the prime minister had not changed and that “of course he should resign”.
A separate inquiry by Durham police into whether Sir Keir broke Covid laws at a Labour campaign event in the city in 2021 remains ongoing.
Sir Keir has pledged he will quit as Labour leader if he receives a Fixed Penalty Notice over that event.
Liberal Democrat leader Sir Ed Davey said: “The full Sue Gray report should now be published without delay, and the parliamentary inquiry should be launched into Johnson’s lies.
“The public made huge sacrifices while Boris Johnson partied. They deserve the full truth.”
The end of the police inquiry means the prime minister has not been fined for a garden party in Downing Street he attended in May 2020, to which about 100 people were invited.
The Met confirmed other people had been fined over their presence at this event.
Mr Johnson has previously apologised for attending the garden party for 25 minutes, saying he “believed implicitly” it was a work event.
The gatherings that resulted in fines took place between May 2020 and April 2021, with different Covid rules in place at different times.
Acting Met Police Deputy Commissioner Helen Ball said whether an event had taken place in “someone’s home” or not had been a factor in deciding whether to issue fines.
The Met said it would not be identifying any recipients of fines from its investigation, which had involved 12 detectives and cost £460,000, and that there had been no interviews under caution.