The Spaniard had already-qualified for the last four but in beating Berdych 6-4 1-6 6-3 he also sent Wawrinka through as Group A runner-up.
Wawrinka had earlier beaten already-eliminated Spaniard David Ferrer in three sets.
The hard-hitting Berdych pushed world number one Nadal hard throughout the match but faded at the end of the deciding set when he double-faulted twice in the eighth game to drop serve.
Nadal then completed victory after nearly two hours of engrossing action with a screaming forehand winner.
Nadal, who has never won the Tour's season-ending showpiece, will face either Swiss six-times champion Roger Federer or Argentine Juan Martin del Potro who meet on Saturday to decide who finishes runner-up in Group B behind Serb Novak Djokovic.