Blinken was already traveling in Southeast Asia for meetings with leaders of the Group of Seven leading industrialized countries and the Asia-Pacific Economic Cooperation group.
Blinken met with Japanese Prime Minister Fumio Kishida and other senior government officials.
"I’m really grateful to him for taking time to see us in this incredibly difficult time," Blinken said afterward. "And the reason we’re here is that President Biden asked me personally on behalf of the president, on behalf of the American people to extend our condolences on the passing of former Prime Minister Abe."
The State Department said earlier in the day that the U.S.-Japan alliance is a "cornerstone" of peace and stability in the Indo-Pacific.
Blinken praised Abe on Monday as "a man of vision."
"I shared with our Japanese colleagues the sense of loss, the sense of shock that we all feel, the American people feel, at this horrific tragedy and killing," the secretary said. "During his time in office, Prime Minister Abe really took the relationship between our countries to new heights."
Abe, 67, was shot and killed at a campaign event in Nara, near Kyoto, on Friday. Blinken has so far been the most senior U.S. official to visit the country since his death.
Biden condemned the attack Friday, calling Abe a "champion of the alliance between our nations and the friendship between our people."
Later in the day, Biden issued a proclamation ordering that U.S. flags be flown at half-staff at the White House and at all government buildings and military bases in Abe's memory.
Blinken's last-minute stop in Tokyo preceded his return to the U.S., which was expected to include a stop in Anchorage, Alaska.