The 14-year-old Si, who looked strangely nonplussed when her triumph at the spectacular hilltop Montjuic pool was confirmed, held her nerve after both she and Chen turned in below-par efforts on the fourth of their five dives.
Si's winning total was 392.15 points, with Chen trailing on 388.70. The 20-year-old again had to settle for silver after she came second in 2007 and 2009 before winning gold in home waters in Shanghai two years ago.
European champion Iuliia Prokopchuk of Ukraine secured the bronze with 358.40 ahead of Britain's Sarah Barrow on 346.45.
"Overall my performance was quite good, especially the first four dives where I was consistent," Si told reporters.
"My secret for success? Train hard and not be lazy."
Twice a double Olympic champion in the 10-metre individual and synchro in Beijing in 2008 and London last year, Chen swept to her fourth 10-metre synchro gold in a row on Monday.
She said having talented team mates was a motivation for her to do better.
"The competition is as it is: someone wins and someone has to lose," she said.
"The key is how you manage your failure. If you keep looking back, you won't do it better. If you look ahead, your failure will just be a bad memory."
Si's success was China's sixth diving gold out of seven on offer so far in Barcelona, with only the men's 10-metre synchro, won by Sascha Klein and Patrick Hausding of Germany, eluding them. They won all 10 diving golds in Shanghai.
There was a surprise in the men's three-metre springboard earlier on Thursday when Olympic champion Ilya Zakharov of Russia failed to qualify for Friday's final.
(Writing by Iain Rogers in Madrid; Editing by Sonia Oxley)
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