Backstage, the Tony Award-winning Chenoweth noted that she is appearing on an upcoming episode of Fox's show Glee, has shot two movies and is doing a series of concerts.
Cryer, whose series is the most-watched comedy on TV, brought a wry tone to his speech.
“I used to think that awards were just shallow tokens of momentary popularity, but now I realize they are the only true measure of a person's worth as a human being,” Cryer said.
The Daily Show with Jon Stewart won the trophy for best variety, music or comedy series, its seventh in a row.
Grey Gardens, the story of a reclusive mother and daughter who were relatives of Jacqueline Kennedy Onassis, and the Dickens adaptation Little Dorrit won for best movie and miniseries, respectively.
Harris, a nominee as well as host, lost to Cryer for his role on How I Met Your Mother but won on-stage accolades for his emcee work, including a heartfelt compliment from Jon Stewart.
Harris, who moved the show along with good-natured humour, started the evening on a lively note, performing Don't Touch That Remote, a custom-made tune from Broadway composers Scott Wittman and Marc Shaiman of Hairspray fame. Harris implored viewers to stay glued to the show and called attention to some of the stars in the house.
“I see legends galore, Lange, Barrymore,” Harris sang to Jessica Lange and Drew Barrymore, later adding, “But like next season on Idol I'm not seeing Paula Abdul.” Meanwhile, the camera panned to an empty seat at the Nokia Theatre.
Harris' winning turn as host also was lauded by Jeff Probst, honoured as best reality show host for CBS' Survivor. Probst was one of the five reality hosts who emceed the Emmys last year and received scathing reviews.
“Neil Patrick Harris, this is how you host the Emmys. Nice job,” Probst said, pointing his Emmy toward him.
The Amazing Race won its seventh consecutive Emmy in the outstanding reality-competition category, once again turning top-rated American Idol into an also-ran.
An exception to the upbeat mood came in clips from animated series Family Guy, which showed the dog character Brian beaten bloody, followed by a reality show snippet with barely concealed swearing.
In a bid to give viewers reasons to stick with the show, CBS put advisories on-screen of upcoming moments, including Justin Timberlake's appearance as a presenter.
The TV academy, meanwhile, hoped to avoid an unwanted rerun at the 61st Annual Primetime Emmy Awards: paltry viewership. The 2008 ceremony was the least-watched ever with an audience of 12.3 million.
Acclaimed but low-rated series like Mad Men are seen as one reason viewers bypassed the awards, so major categories were expanded to increase the odds for more popular fare. There were as many as seven nominees per category, compared with the traditional five.
Harris and Emmy executive producer Don Mischer promised to keep the scheduled three-hour ceremony snappy, but they had less room to manoeuvre than planned. A TV academy proposal to pre-tape some acceptances and show them in a truncated version — gaining time for something more entertaining than speeches — was quashed by industry opposition.
HBO went into the ceremony as the awards leader after last weekend's Creative Arts Primetime Emmys ceremony for technical and other achievements. The channel earned 16 trophies, followed by NBC with 11 and Fox and ABC with eight awards each. CBS, PBS and Cartoon Network had six each.
After Sunday, HBO emerged with a leading 21, followed by NBC with 16, ABC with 11 and Fox with 10. CBS and PBS had nine each.
LIST OF WINNERS
* Drama Series: Mad Men, AMC.
* Comedy Series: 30 Rock, NBC.
* Actor, Drama Series: Bryan Cranston, Breaking Bad, AMC.
* Actress, Drama Series: Glenn Close, Damages, FX Networks.
* Actor, Comedy Series: Alec Baldwin, 30 Rock, NBC.
* Actress, Comedy Series: Toni Collette, United States of Tara, Showtime.
* Supporting Actor, Drama Series: Michael Emerson, Lost, ABC.
* Supporting Actress, Drama Series: Cherry Jones, 24, Fox.
* Supporting Actor, Comedy Series: Jon Cryer, Two and a Half Men, CBS.
* Supporting Actress, Comedy Series: Kristin Chenoweth, Pushing Daisies, ABC.
* Miniseries: Little Dorrit, PBS.
* Made-for-TV Movie: Grey Gardens, HBO.
* Actor, Miniseries or Movie: Brendan Gleeson, Into the Storm, HBO.
* Actress, Miniseries or Movie: Jessica Lange, Grey Gardens, HBO.
* Supporting Actor, Miniseries or Movie: Ken Howard, Grey Gardens, HBO.
* Supporting Actress, Miniseries or Movie: Shohreh Aghdashloo, House of Saddam, HBO.
* Directing for a Comedy Series: The Office: Stress Relief, Jeff Blitz, NBC.
* Directing for a Drama Series: ER: And in the End, Rod Holcomb, NBC.
* Directing for a Variety, Music, or Comedy Series: American Idol: Show 833 (The Final Three), Bruce Gowers, Fox.
* Directing for a Miniseries, Movie, or Dramatic Special: Little Dorrit: Part 1, Dearbhla Walsh, PBS.
* Variety, Music, or Comedy Series: The Daily Show With Jon Stewart, Comedy Central.
* Reality-Competition Program: The Amazing Race, CBS.
* Writing for a Comedy Series: 30 Rock: Reunion, Matt Hubbard, NBC.
* Writing for a Drama Series: Mad Men: Meditations in an Emergency, Kater Gordon and Matthew Weiner, AMC.
* Writing for a Variety, Music, or Comedy Series: The Daily Show With Jon Stewart, Comedy Central.
* Writing for a Miniseries, Movie, or Dramatic Special: Little Dorrit, Andrew Davies, PBS.
* Host, Reality or Reality-Competition Program: Jeff Probst, Survivor, CBS.
* Original Music and Lyrics: 81st Annual Academy Awards: Song Title: Hugh Jackman Opening Number, ABC.