Mr Abe and his wife Akie arrived at the head of a 17-strong motorcade at the memorial site where the six-storey CTV Building stood in Christchurch before it came down in the violent February 22 tremor, which claimed 115 lives.
They were met by Earthquake Recovery Minister Gerry Brownlee and Canterbury Earthquake Recovery Authority boss Roger Sutton.
Mr and Mrs Abe laid a wreath at the cleared site, which is now a place of remembrance, before a respectful bow.
A crowd of around 50, mostly Japanese, shouted and waved from behind the security cordon. They were excited to shake hands with the world leader.
They then watched the couple cross Madras St for a short tour of the "cardboard" Transitional Cathedral -- the temporary place of worship built after the landmark Christ Church Cathedral was badly damaged in the magnitude-6.3 shaking.
Of the 185 people killed in the quake, 115 perished in the CTV building.
In February, just after the third anniversary of the disaster, families of the Japanese CTV victims were given a private briefing by police and Ministry of Business, Innovation and Employment officials on progress of the police probe into the collapse.
After the cathedral visit, Mr Abe, the first Japanese prime minister to visit New Zealand since Junichiro Koizumi in 2002, was chauffeur-driven to the military terminal at Christchurch International Airport to fly to Australia.