13% is the reduction in all-cause mortality — ie, if every death this prevented was a death from malaria, this reduced deaths from malaria by over 99%.
This would mean that a lot of malaria related deaths are unaccounted for or that the vaccine is helping in another way.
One hypothesis is that some people who caught malaria but did not die from malaria, did die more frequently to another cause where having had malaria was a contributing factor to that death.