Paltrow took home the award for 'Outstanding Guest Actress in a Comedy Series' for her role as Holly Holliday on Glee, while Timberlake received 'Outstanding Guest Actor in a Comedy Series' for his work on NBC's Saturday Night Live.
Paltrow was unable to attend the awards ceremony, having to stay in London to look after her children.
Loretta Devine won 'Outstanding Guest Actress in a Drama Series' for her role as Adele Webber on Grey's Anatomy, and Paul McCrane landed 'Outstanding Guest Actor in a Drama Series' for playing Assistant D.A. Josh Peyton on Harry's Law.
Among other winners last night were Jeff Probst, who won his fourth 'Best Reality Show Host' for Survivor, and Futurama for 'Outstanding Animated Programme'.
HBO took home 15 awards over the course of the evening, with Boardwalk Empire picking up seven in total, including 'Best Art Direction' and 'Best Picture Editing'.
The Creative Arts Emmy Awards are scheduled to air on Reelz Channel on September 17, while the Primetime Emmy Awards will air live on Fox on September 18.
Watch a clip of Gwyneth Paltrow's award-winning guest role on Glee below: