Skyteam member China Eastern has very low economy fares for flights from San Francisco to Japan via one-stop Shanghai. SFO-FUK Fukuoka is as low as $469 round trip and Tokyo as low as $483 round trip. The catch is most itineraries require you spend the night in Shanghai PVG on the outbound legs. Some itineraries mean overnight in Shanghai on return too.
Departure dates are from late February into April. There are lots of available dates with more low fare dates on weekends to Fukuoka than Tokyo.
These China Eastern low fares book in economy Q, which is an ineligible fare code for earning miles in Delta SkyMiles.
China Eastern San Francisco SFO – FUK Fukuoka, Japan
$468.86 Tuesday March 8 – Tuesday March 15
China Eastern San Francisco SFO – NRT Tokyo, Japan
$482.96 Wednesday March 9 – Saturday March 19
Sometimes a low fare is simply a low fare deal without miles earning.