Puerta, one of Spain's most promising young players, died aged 22 after helping the Andalucian club win back-to-back UEFA Cups and their fourth King's Cup. His wife later gave birth to their son, Aitor.
Captain and goalkeeper Andres Palop wore a T-shirt with Puerta's name on as he accepted the huge silver cup from the Prince of Asturias and coach Antonio Alvarez said Puerta had been with the team in spirit.
"This title is also for Puerta, and for all those who are no longer with us," Spain winger Jesus Navas, who sealed the 2-0 win over Atletico Madrid at the Nou Camp with a breakaway goal in added time, said in a television interview.
"We were in debt to him (Puerta) and we wanted to celebrate a title for him," president Jose Maria del Nido said.
The club's thoughts also turned to defender Sergio Sanchez, who was ordered to stop playing by doctors in January after being diagnosed with a heart condition and is set to have surgery in a bid to save his career.
Puerta was a product of Sevilla's youth system, breaking into the first team in the 2004-5 season before becoming a regular the following year as a versatile left-sided player who could play as a wing back or midfielder.
He was fondly remembered for the spectacular goal he scored against Schalke 04 that put the club in the UEFA Cup final for the first time in April 2006 and earned him one cap for Spain.
Del Nido said the cup victory and Sevilla's qualification for next season's Champions League thanks to their fourth-placed finish in La Liga cemented the club's position as one of the top sides in Europe.
"We have a project that we started seven years ago and that is now a reality," he told TVE television. "Let's see what we can achieve next season."
