It was the latest clash between the two Jamaican stars ahead of the London Olympics, where Bolt's supremacy in the sprinting world appears to be in danger.
Bolt finished second in 19.83 while Warren Weir also earned a ticket to the London Games by finishing third.
"I have been working hard and am seeing it paying off now," Blake said.
"I was not surprised by the big win. I know what Bolt has to offer and I know he was not at 100 percent. I just tried to keep my form."
Blake had won his 200m semi-final in 19.93 seconds Saturday to set up another finals showdown with Bolt, who took his semi-final race in 20.26.
Blake produced his first upset of the weekend and one of the biggest in the sport this year by beating Bolt in Friday's 100m final with a time of 9.75 seconds, becoming the fourth fastest man ever in the event.
Bolt, the 100m and 200m Olympic champ and world record holder, was second in 9.86 seconds after a poor start and Asafa Powell was third in 9.88 seconds.
"I can't train for one person," Bolt said Sunday. "No one was talking about Blake and see what he did."
Bolt says he now has plenty to prove heading into the Olympics and vowed to come back from these defeats.
"I am the Olympic champion and I have to show the world I am the best," Bolt said. "I will always make a comeback. It is not like I was blown away. I know what I need to do to get it right."
Blake ran the world-leading time on Sunday in the 200m but he did not beat his personal best of 19.26 which he set in September 2011.
Neither Blake nor Bolt have committed to running both sprints in London, saying they will leave the decision up to their Jamaican coach Glen Mills.
Blake said he was not surprised by the weekend results, adding he "worked hard" to get in top form.
Bolt is confident he can get up to speed with an accelerated training regime leading up to the Summer Olympics.
"It's all about work and just needing to get my things together and get it right," Bolt said. "I got to get in the work and figure out what I did wrong.
"I have to work hard to get ready for the Olympics. I think I am a little bit weak but three more weeks should be good enough to get back into shape."
Still questions will surround Bolt who had to receive medical treatment briefly on the track at National Stadium after crossing the finish line Sunday. Trainers worked on his legs before Bolt got up and walked off the track.
Weir's third place finish (20.03) was also a surprise as he beat out Ashmeade Nickel (20.16) for a Games' spot.
On the women's side, Shelly-Ann Fraser-Pryce was also a double weekend winner as she clocked a personal best 22.10 in the 200m, ahead of Olympic silver medalist Sherone Simpson (22.37) and Veronica Campbell-Brown, who was third with a time of 22.42.
"I am tired," said Fraser-Pryce. "It is a personal best. Today was about execution and not winning but I am glad for the win."