We demonstrate that rectification ratios (RR) of >250 (>1000) at biases of 0.5 V (1.2 V) are achievable at the two-molecule limit for donor-acceptor bilayers of pentacene on fullerene on Cu using scanning tunneling spectroscopy and microscopy. Using first-principles calculations, we show that the system behaves as a molecular Schottky diode with a tunneling transport mechanism from semiconducting pentacene to Cu-hybridized metallic fullerene. Low-bias RRs vary by two orders-of-magnitude at the edge of these molecular heterojunctions due to increased Stark shifts and confinement effects.