Despite rainy weather, residents and tourists gathered around the 634-metre (2,080-foot) tower and its adjacent shopping and amusement complex which also opened on Tuesday.
But those hoping for spectacular views from the observation deck 350 metres up were thwarted by the weather.
“I have long been looking forward to coming here,” said Ayumi Nakazawa, who won tickets to the opening ceremony of the tower, which ranks as the world’s second-tallest structure.
“I can’t see the view (because of the rain), but it was exciting,” Nakazawa told reporters after becoming the first official visitor to the observation deck.
Japan’s hard-hit tourism sector is hoping the tower will boost the number of visitors from abroad after figures plummeted in the wake of Japan’s quake-tsunami disaster last year.
The Tokyo Skytree is the world’s second-tallest manmade structure, topped only by the 828-metre Burj Khalifa in Dubai.
It stands taller than the 600-metre Canton Tower in the southern Chinese city of Guangzhou and the 553-metre CN Tower in the Canadian city of Toronto.
In Japan’s capital the Tokyo Skytree overshadows landmarks in the upscale western district including the 333-metre Tokyo Tower, which was built in 1958 and became a byword for the country’s rapid post-war growth.