The creative arts awards, held Sunday night, recognized technical and other achievements for the 2003-04 season.
Both Stone and Shatner were honored for guest appearances in "The Practice," a popular television series. Shatner is reprising his character, attorney Denny Crane, in "Boston Legal," a reworked version of the drama debuting next month.
For guest actor and actress in a comedy series, the winners were Laura Linney for "Frasier," a sitcom, and John Turturro for "Monk," a comedic drama.
Honors for best comedy and drama series, best movie and other achievements will be given Sunday, Sept. 19.
In August, Dan Castellaneta, the voice of Homer Simpson, was awarded an Emmy for voiceover performance during a ceremony honoring achievements in animated programs and costumes.
It was the third Emmy for Castellaneta, who won back-to-back statuettes in 1992 and 1993 for his work on "The Simpsons."
"My Life as a Teenage Robot" background stylist Seonna Hong drew the animation nod. Hong was recognized for the Nickelodeon cartoon's episode "The Wonderful World of Wizzley."
As for variety/music costumes, Emmys went to "Smucker's Stars on Ice 2004" costume designer Jef Billings and costume supervisor Regina Winters.