Jota and his brother, fellow footballer Andre, were reportedly killed in the province of Zamora, Spain, on Thursday after a car collision.
The former Atletico Madrid and Wolves star married the mother of his three children just five days ago.
A Premier League champion last season, Jota also won the Nations League last month with Portugal and earned 49 caps for his country, scoring 14 goals.
Following the shocking news, tributes have been pouring in from around the football world, with fans laying flowers outside Anfield.
In a statement, the Portuguese Football Federation said: "The Portuguese Football Federation and all of Portuguese football are completely devastated by the deaths of Diogo Jota and his brother Andre Silva, this morning, in Spain.
"Much more than an outstanding player, with nearly 50 caps for the National A Team, Diogo Jota was an extraordinary person, respected by all colleagues and opponents, someone with a contagious joy and a reference in his own community.
"The Portuguese Football Federation expresses its deepest condolences to the family and friends of Diogo and Andre Silva, as well as to Liverpool FC and FC Penafiel, the clubs where the players respectively played."
His club Liverpool said in a statement: "Liverpool Football Club are devastated by the tragic passing of Diogo Jota.
"The club have been informed the 28-year-old has passed away following a road traffic accident in Spain along with his brother, Andre.
"Liverpool FC will be making no further comment at this time and request the privacy of Diogo and Andre's family, friends, teammates and club staff is respected as they try to come to terms with an unimaginable loss.
"We will continue to provide them with our full support."
Liverpool teammate Stefan Bajcetic, who spent last season on loan at Las Palmas, was the first current player from the Reds to release a comment, posting an image in training with Jota on Instagram with the caption: "You will be remembered my friend."
Clubs around the Premier League all paid their respects via their social media channels, as well as sides across Europe.
Portugal teammate Cristiano Ronaldo posted a short tribute via his Instagram account, expressing his deep shock at the tragic news.
"It doesn't make sense," Ronaldo said.
"Just now we were together in the National Team, and just now you've gotten married.
"To your family, your wife and your children, I send my condolences and wish you all the strength in the world. I know you'll always be with them. Rest in peace, Diogo and Andre. We'll all miss you."
Wolverhampton Wanderers, who first brought the forward to England in 2017, said they were "heartbroken".
"Diogo was adored by our fans, loved by his teammates and cherished by everyone who worked with him during his time at Wolves. The memories he created will never be forgotten.
"Our hearts go out to the family, friends and loved ones of Diogo and his brother, Andre.
"You will be truly missed, and always remembered.
"Our deepest condolences are with the loved ones of Diogo Jota and his brother, Andre, and everyone connected with Liverpool FC following today's heartbreaking news," Manchester United said on X, while Liverpool's neighbours Everton posted: "Everyone at Everton is deeply saddened by the tragic passing of Diogo Jota and his brother André Silva.
"Our thoughts are with their family and friends at this sad time."
The Premier League said via a post on X that football "has lost a champion."
"Everyone at the Premier League is shocked and devastated to learn of the tragic passing of Diogo Jota and his brother Andre," the statement said.
"Our sincerest condolences go to Diogo's family, friends, Liverpool FC, and all their supporters at this heartbreaking time. Football has lost a champion who will be forever missed. We will continue to support our friends and colleagues at the club.
Portuguese football club Porto, a club both brothers played for at some point in their careers, said they are in "mourning" over the deaths.
"It is with shock and deep sorrow that we extend our heartfelt condolences to the family and friends of Diogo Jota and his brother André Silva, who was also our athlete in the youth ranks," the club wrote in a post on social media.
"Rest in peace," they added, adding an image of the brothers in their Porto kits.
"Devastating news about Diogo Jota and his brother Andre this morning," former Liverpool defender and Sky Sports pundit Jamie Carragher posted on X.
"Thoughts are with every one of their family and friends, especially his wife Rute and their three lovely kids."
Jota's former Wolves teammate Ruben Neves posted a short tribute on his Instagram: "They say we only lose people when we forget them. I will never forget you!"