At 31, Nadal becomes the oldest ITF men's world champion after a season in which he won a 10th French Open and a third US Open.
The Spaniard also became the oldest player to finish the year at No. 1 since the ATP rankings began in 1973.
Muguruza dropped only one set en route to her first Wimbledon title and finished the year at No. 2 behind Simona Halep.
"Becoming ITF world champion in such a competitive year is amazing for me," said Muguruza, who is also Spanish. "(Nadal) is a great role model for all of us, so it is a great moment for tennis in Spain."