Singers Suresh Wadkar and Adnan Sami as well as veteran TV actor Sarita Joshi have also been conferred with the fourth highest civilian honour of the country.
Karan and Ekta said they were humbled to receive the honour.
"Overwhelmed by so many emotions right now. Humbled, elated and also thankful for the opportunity to live my dream everyday, to create and to entertain. I know my father would be proud and I wish he was here to share this moment with me," he said in a statement posted on Twitter.
Son of veteran Bollywood producer late Yash Johar, Karan Johar started his career as a director in Hindi cinema with the 1998 hit Kuch Kuch Hota Hai .
The 47-year-old, who runs Dharma Productions, went on to direct several commercial blockbusters in Kabhi Khushi Kabhie Gham (2001), My Name Is Khan (2010), Student of the Year (2012) and Ae Dil Hai Mushkil among others.
Karan has also produced several critically-acclaimed films -- Wake Up Sid, Agneepath, Hasee Toh Phasee, Kapoors & Sons and Raazi.
Ekta, who started her showbiz journey with soap operas, most notably Kyunki Saas Bhi Bahu Thi, is the daughter of veteran actor Jeetendra.
She launched her banner Balaji Telefilms in 1994 and backed many popular TV shows, eventually branching out into movie production.
Ekta, 44, has produced films such as Love Sex Aur Dhoka, Once Upon a Time in Mumbai, The Dirty Picture, Udta Punjab and Veere Di Wedding.
"My foray into the industry started when I was just 17. I constantly heard I was 'too young', 'too raw' and it was 'too soon' to make things happen. Through the years I've realised it's never 'too soon' to live out your dreams and being 'too young' is probably the best thing," she said.
"Today, as l'm conferred with the 4th highest civilian honour- Padma Shri', I'm humbled. I hope to continue breaking boundaries, to continue giving young talent a chance and to strive to give back to the country for all the love that's come my way.
The timing couldn't have been more perfect, as this news arrives 2 days before my son's first birthday. Grateful & Thankful!" she added.
Kangana, a three-time National Award Winner, is the only Bollywood actor to receive the Padma Shri this year.
The 32-year-old, who made her debut in movies in 2006 with Gangster, is regarded as one of the most successful female artistes of this generation.
After a series of films with Mahesh Bhatt's banner, she found success with Madhur Bhandarkar's Fashion, for which she won her first National Film Award in 2009.
She went on to win two back-to-back National Film Awards for her performances in Queen (2014) and Tanu Weds Manu Returns (2015). Kangana's latest release is Panga.
Wadkar, 64, a veteran in the music industry, started his career as a playback singer in 1978 with song Seene mein jalan for Gaman. He has lent his voice to memorable tracks like Aye zindagi gale lagaa le, Aur is dil mein, Pardesi pardesi, Sapne mein, Raat ke dhai baje and Jag Ja.
In his over four-decade-long career, Wadkar has collaborated with celebrated composers RD Burman, Shiv-Hari, Ilayaraja, Khayyam, AR Rahman, Bappi Lahiri, Vishal Bhardwaj and Hridayanath Mangeshkar.
Sami, 48, now an Indian-citizen, made a mark for himself in country's indie-pop scene with single Kabhi toh nazar milao, for which he collaborated with veteran playback singer Asha Bhosle.
"The greatest moment for any Artiste is to be appreciated & recognised by his/her government. I am overwhelmed with infinite gratitude for being honoured with the 'Padma Shri' by the Government of India. It has been a 34 years musical journey.. 'Bohot Shukriya'!!" Sami tweeted,
He released various albums in the early 2000s and also served as music composer for films Lucky: No Time for Love (2005), Dhamaal (2007) and Shaurya (2008).
Sami, born in London to a Pakistani Air force veteran, applied for Indian citizenship in 2015 and became a citizen of the country in January 2016.
Joshi, a household name and a popular theatre personality, started her acting career as a child artiste and made her TV debut in 1980s with Titliyan .
Some of her most iconic shows are Hasratein , Ek Mahal Ho Sapno Ka , Baa Bahoo Aur Baby and Bh Se Bhade .
Joshi, 78, has also featured in movies such as Nazar , Darna Zaroori Hai , Dasvidaniya , Singham Returns and Simmba .
She was bestowed with the Sangeet Natak Akademi award for acting in Gujarati in 1988.
"I am very happy and humbled with this honour. I am working from an early age, I have never worked for awards, for me work is worship. I have always worked from heart and given my best in whatever I have done. I will be known as Padma Shri Sarita Joshi, this is such a big honour. I am happy as my children are happy," Joshi told PTI.
The Padma Shri for this year has been awarded to a total of 118 eminent personalities across fields of art, literature and education, medicine, trade and industry, sports, public affairs, social work and science and engineering.