Good responsiveness of autonomous vehicle computing systems is crucial to safety and performance of the vehicles. For example, an autonomous vehicle (AV) may cause an accident if the end-to-end latency from sensing a pedestrian to emergency stop is too high. However, the AV software stacks are too complex to probabilistically analye the end-to-end latency on a multi-core system. They consist of a graph of tasks with different periods, and have a large variability in the task execution times, which may lead to the maximum core utilization Umax >= 1.0 on some cores. This paper proposes a novel stochastic analysis of the end-to-end latency over the AV stacks that allows Umax to exceed 1.0 on each core. The proposed analysis models the entire stack as a graph of task graphs under a multi-core partitioned scheduling and provides a probabilistic guarantee that the analyzed latency distribution upper-bounds the one observed from a real system under the assumption of independent task execution times. Using the Autoware stack with inter-task dependent execution times, it is shown that our analysis, combined with a task grouping to mitigate the inter-task correlations, can give a latency distribution for each task path that almost upper-bounds the observed one.