Two bus trips are featured. Bruce Korusek identifies the bus in the first scene (Ross rides, Hoffman runs after it and eventually gets on) as an AC Transit GM New Look bus.
At the end of the film, Hoffman and Ross ride off on a GM old look bus.
Saul Daniels pointed me to some useful information on the bus used at the end of the movie. What is seen on screen is a yellow 1956 GMC TDH4512 fleet number 4522 in the livery of 'Santa Barbara Municipal Bus Line'.
The bus line is fictional, the bus was actually a Santa Monica Municipal Bus Line vehicle repainted for the movie. Although the movie was shot in 1966, it was released in 1967, by which time the bus had been sold to Campus Bus Service, Kent State University. When its identity was discovered, the bus, numbered 2345 with CBS, was christened 'The Graduate', and after retirement from active service was preserved by Bill Schloman.