I believe the term spontaneous generation concerns the very first organism from which every other organism supposedly evolved. Where did the first organism come from? It spontaneously generated! Sure, but that's outside of the field of study of evolution (although there is certainly interest in it from the evolutionary research community). Evolution deals with how things change generation-to-generation while reproducing themselves. By definition, abiogenesis (literally, "life's origin") itself is a different field of study, which worked by different "rules" than those which govern evolution.
It's a fundamental shift in processes that occurs once replication manages to occur for the first time (however it occurs). Evolution would remain a valid explanation for how modern life came to be no matter how the first *seed* was planted (e.g. by God, by chance, by aliens starting a science project, by a meteorite bringing simple life from another planet, etc.)
Additionally, you have a misconception in your wording. You write of the first "organism", but most likely (i.e. according to the best research as it now stands) the first successful replicator would likely have more resembled an autocatalytic collection of chemicals than anything we would call an "organism". But evolution works on replicators of any kind to improve and refine them, not just those that are undeniably "living", and thus the first replicator would eventually be honed by evolution into complex enough systems that they would later be rightful subjects of the title "organism". Creationists grossly distort the picture when they try to imply that scientist believe that life took a sudden leap from a soup of random chemicals to something resembling a modern cell, *poof*. There are many stages in between.