He was attacked when he had stepped out of his office in Press Colony in the city to head home.
"Pakistan strongly condemns the targeted killing of renowned Kashmiri journalist, Shujaat Bukhari and his guard in Srinagar, IOK today", the Foreign Office Spokesperson Dr Faisal tweeted. A security guard protecting him and his driver were also shot.
"He (Bukhari) is no more".
Shujaat Bukhari, who was in his 50s, was given police protection since an attack on him in 2000.
"Assassination of #ShujaatBukhari is a brutal attack on freedom of press. My deepest condolences to his family", Mehbooba tweeted.
BJP's Ram Madhav said, "Shocked to hear about d attack on d Editor-in-Chief of Rising Kashmir Shujaat Bukhari in Srinagar".
India's interior minister Rajnath Singh called Bukhari's killing "an act of cowardice", while Rahul Gandhi, the leader of the country's main opposition Congress party, tweeted that Bukhari was "a courageous heart who fought fearlessly for justice and peace".
"This is why any resolution of the political situation in Kashmir must entail a commitment to end the cycles of violence and ensure accountability for past and current violations and abuses by all parties, and provide redress for victims", he said.
The International Federation of Journalists (IFJ) report released in December last year said that the media in Jammu and Kashmir has "walked the razor's edge" for the past 30 years, facing pressures from all sides of the conflict. He was instrumental in organising several conferences for Kashmir peace.
Chief Minister Mehbooba Mufti visited the family journalist Shujaat Bukhari. He was also part of the Track II process with Pakistan.