The 27-year-old confirmed that she will miss the event in the summer but she hopes to defend her Olympic heptathlon title in Rio 2016.
She said in a statement, "I have some very unexpected but exciting news to share - Andy and I are expecting a baby.
"We are completely overwhelmed, with excitement and a degree of anxiety that I am sure all first time parents will relate to.
"My plans for 2014 have been completely turned upside down, but having had a couple of weeks to think about things from a career point of view I am 100 per cent set on returning to full time athletics once our baby is born and go for a second gold medal at the Rio Olympics in 2016 - that challenge really excites me.
"But in the short term I will make our baby a priority and enjoy the whole experience as much as possible.
"I am sorry I won't be in Glasgow for the Commonwealth Games, but know it will be an amazing occasion. I will be at home awaiting the arrival of a little Ennis-Hill."
She joins a list of other big name athletes who will miss the competition. Olympic cyclist Sir Chris Hoy retired last summer and will not compete in the veldrome which is named after him while track runner Mo Farah has said he is focusing on training for the London Marathon and is unlikely to compete at the Commonwealth Games.
The news that Ennis-Hill will miss the Commonwealth Games means the athletics crowds in Glasgow will be denied the sight of an athlete whose triumph at London 2012 proved one of the highlights of the last Olympics.
The world's leading all-round athlete claimed gold in dazzling fashion and was expected to repeat the feat in Glasgow, where she would have been seeking her first Commonwealth Games title.
She took bronze in Melbourne in 2006, when Kelly Sotherton won gold, but skipped the 2010 Games in Delhi where fellow English athlete Louise Hazel triumphed, preferring to compete at the European Championships.
Ennis-Hill landed the 2010 European gold before finishing second at the 2011 World Championships, behind Tatyana Chernova.
London was a different story, with Ennis-Hill a resounding winner with a personal best score for the seven-event competition.
However, she has barely competed since the Olympics, being forced to miss last summer's World Championships in Moscow due to an Achilles injury.
While Ennis has set the Rio de Janeiro Games in 2016 as her goal, fellow heptathlete Louise Hazel believes there must be some doubt over the Yorkshire athlete staying in the multi-discipline event.
Hazel said: "Is it possible to be an elite sportswoman and have a baby? Yes. Is it possible to come back from Olympic gold as a heptathlete and go on to Rio... it throws a huge question over the continuation of a career as a heptathlete and that's just being realistic.
"I think she'll be able to come back and compete. The question is: in what event?
"Will she be able to get back to the same form she's been showing in recent years and be competitive?
"You have to look at people like Katarina Johnson-Thompson, who's been breaking Jess' junior records non-stop."
Hazel, who retired from heptathlon but is planning to continue her athletics career in other events, is backing 21-year-old English athlete Johnson-Thompson to claim the Commonwealth title.
"One hundred percent," Hazel told Sky Sports News. "I'm hoping I can pass my heptathlon crown over to Katarina, the weight of expectation is on her shoulders so no pressure. I think she can do it."
There remains doubt over whether Jamaica's world-leading sprinter Usain Bolt will compete in Glasgow, as he maps out his schedule for the year, while Mo Farah has yet to commit.
Games officials remain hopeful both superstar track athletes will appear, and were quick to send best wishes to Ennis-Hill.
A note on the official Glasgow 2014 Twitter page read: "Congratulations to #Glasgow2014 ambassador @J_Ennis & husband Andy on the exciting news that they're expecting their first child."