The team of the year award went to Europe's Ryder Cup team after their stunning victory over the United States at Medinah last September.
Great Britain won three prizes with Ennis, Andy Murray and Sebastian Coe all taking home awards.
Ennis dominated the Olympic heptathlon and won the gold medal despite carrying the enormous pressure of home hopes at the Olympic stadium, while Murray won the breakthrough award after winning his first Grand Slam at the US Open as well as Olympic gold and silver medals in London.
Coe, the chairman of the Organising Committee of the London Olympic and Paralympic Games and also a Laureus World Sports Academy Member, received the lifetime achievement award.
Bolt, who also won the award in 2009 and 2010, won gold in the 100, 200 and 4x100 metres relay in London to repeat his medal haul from Beijing. He was not there in person to receive the award at Rio's Theatro Municpal but appeared via a hologram.
Wearing a suit and tie and holding the trophy in his hands, Bolt promised to defend his Olympic titles at the 2016 Rio Games.
"Definitely I will be here in 2016," he said.
Also nominated for the award was American swimmer Michael Phelps, who won four gold and two silver medals in London to become the most decorated Olympian of all time.
Phelps was given a new award for Exceptional Achievement, which he collected at the gala ceremony in the 2016 Olympics host city just hours after participating in a swimming class for children at a Rio slum.
"Being able to be given an award from athletes who are icons in their sports, it's just a tremendous honour," Phelps said. "My life just keeps getting better and better."
Also nominated for the top sportsman award were British Olympic champions Mo Farah and Bradley Wiggins, Formula 1 triple world champion Sebastian Vettel and Barcelona's Lionel Messi.
Dominican Republic's Felix Sanchez received the comeback of the year award after winning the Olympic 400 metres hurdles gold medal in London, eight years after winning it for the first time in Athens.