The Prime Minister revealed the news while leading tributes to the late MP who was killed after a knife attack on Friday.
Addressing MPs, Mr Johnson said parliament had lost a "steadfast servant" while his family has lost a loving husband and devoted father.
He said: "Sir David was taken from us in a contemptible act of violence, striking at the core of what it is to be a Member of this House and violating the sanctity both of the church in which he was killed and the constituency surgery that is so essential to our representative democracy.
"But we will not allow the manner of Sir David’s death to in any way detract from his accomplishments as a politician or as a human being.
"Because Sir David was a patriot who believed passionately in this country, in its people, in its future.
“He was also one of the nicest, kindest, and most gentle individuals ever to grace these benches.
“A man who used his decades of experience to offer friendship and support to new members of all parties.”
There was also applause in the chamber as the Prime Minister confirmed Southend would become a city.
He said: “Behind the famous and irresistible beam lay a seasoned campaigner of verve and grit whether he was demanding freedom for the people of Iran or courting votes in the Westminster Dog of the Year contest whether he was battling for Brexit or fighting his way to the front of the Parliamentary Pancake Race.
“And as every member of this House will know, and you just confirmed Mr Speaker, he never once witnessed any achievement by any resident of Southend that could not, somehow, be cited in his bid to secure city status for that distinguished town.
“Highlights of that bulging folder included a world record for playing most triangles being played at once; a group of stilt-walkers travelling non-stop from the Essex coast to Downing Street; and a visiting foreign dignitary allegedly flouting protocol by saying he liked Southend more than Cleethorpes.
“A compelling case, Mr Speaker, and as it is only a short time since Sir David last put that case to me in this chamber, I am happy to announce that Her Majesty has agreed that Southend will be accorded the city status it so clearly deserves.”
Sir Keir Starmer welcomed the tributes to Sir David, saying each painted its "own picture of a committed public servant, of kindness and of a man whose decency touched everybody that he met".
The Labour leader continued:“Sir David was a dedicated parliamentarian and his loss is felt profoundly across this House.
“We are united in our grief at this terrible time.
“We are thinking – once again - of our dear friend Jo Cox, who was killed just five years ago and I know that Honourable members and their staff will have spent the weekend worrying about their own safety.
“The emotion is the same across the House. But I remember how acutely Jo’s loss was felt on these benches. So today, on behalf of the entire Labour Party, I want to reach across the aisle and acknowledge just how deeply the pain is felt on the benches opposite.
“Of course our differences matter, after all, that’s what democracy is about. But today we are reminded that what we have in common matters far more.”
Sir Keir added he was “so pleased” at the announcement of Southend becoming a city, telling the Commons: “It is a fitting tribute to Sir David’s hard work, it really is.
“Fitting, because David delivered for the causes he championed.”
Sir Keir said the threats and violence against politicians must be confronted in the coming days and weeks, adding: “It is too early for us to comment on the exact motivations and circumstances of David’s killing. But I want to finish by saying this: a cowardly attack on a public servant doing their job, is an attack on our country and our way of life.
“A way of life that prizes tolerance, democracy and respect. That accepts our differences – but cherishes our commonalities. That refuses to succumb to the poison of extremism. No matter what perverted cause, faith or ideology these attackers support, their intention is always the same – to sow division among us.
“That is why our response must always be to show we will never be cowed, that our bonds to one another cannot be eroded, that the hatred that took Sir David’s life will never win.”
The SNP's Westminster leader Ian Blackford claimed Sir David was above all else was a "good and a deeply decent man".
He said: MPs: "We are gathered here united in mourning and grief at the loss of a proud champion of Southend, now to be the city of Southend."
"Members of this house are being murdered while simply doing their job. That is the terrible reality we are faced with. We need to put an end to it together.
"The devastating loss of Sir David has once again laid bare that twin threat of terrorism and the toxic culture of hate and intolerance that has become all too common."
Conservative former minister Mark Francois described Sir David as his “best and oldest friend in politics”.
He continued: “I confess I am hurting terribly so I hope the House will therefore forgive me if because of that my contribution this afternoon is even more incoherent than usual.
“Everything I ever learned about being a constituency MP I learnt from David Amess. He sponsored me for the candidates’ list and he mentored me when I arrived.
“Without him I would never have become a Member of Parliament, so some might well argue he has much to answer for.”