Almunia joined Watford last summer on a 12-month deal after leaving Arsenal and he made 43 appearances for the Championship club.
He played an integral role in Watford finishing third in the table before impressing in the play-off final defeat by Crystal Palace at Wembley.
The 36-year-old had been considering his options and the Spaniard had been linked with a return to La Liga amid reports of interest from Valencia.
However, he has decided to sign a new one-year deal at Vicarage Road and Zola is delighted that Almunia will be part of his plans for the 2013/14 campaign.
"It's fantastic that Manuel has signed a new contract for next season," Zola told the club's official website.
"His experience and influence are so important for us and the impact he had at Watford last season was magnificent."