Elías entered the 125cc World Championship in 2000 at the age of seventeen. In 2001 he finished third in the class and took his first victory at the prestigious Dutch TT at Assen. He moved to the 250cc class for 2002, finishing fourth that year, third in 2003, and fourth again in 2004, establishing himself as a consistent front-runner without quite converting his pace into a title.
In 2005 Elías entered MotoGP for the Fortuna Yamaha team. For 2006 and 2007 his Fortuna backing secured him a seat with Gresini Honda alongside 2005 MotoGP runner-up Marco Melandri.
His defining moment in MotoGP came on 15 October 2006 at the Portuguese Grand Prix at Estoril. Starting the final lap in third position, Elías executed an aggressive braking move into the first corner to pass both Valentino Rossi and Kenny Roberts Jr. and take the lead. Rossi repassed him at the chicane near the end of the lap and appeared to have secured the victory, but Elías used the draft on the run to the final corner, drew level with the Italian, and was awarded the race win by 0.002 seconds — one of the closest finishes in MotoGP history. It was Elías's first and only premier-class victory, and notably cost Rossi the points margin that proved decisive in the 2006 championship, which ultimately went to Nicky Hayden. Elías was the last non-factory rider to win a MotoGP race until Jack Miller's victory for Marc VDS at the 2016 Dutch TT.
He crashed at Assen in 2007, breaking his leg and disrupting his season. In 2008 he raced for Alice Ducati before returning to Gresini Honda for 2009. His results in MotoGP outside of Estoril 2006 were modest, and he never again threatened for a race victory in the premier class.
For 2010 Elías moved down to the newly created Moto2 class on a Moriwaki bike for Gresini. A heavy crash in pre-season threatened his title challenge but he recovered strongly. He won at Le Mans in a chaotic race, took the championship lead, and held it from that point forward, clinching the inaugural Moto2 World Championship at the Malaysian Grand Prix with three rounds to spare — the first and, at the time, only title of his Grand Prix motorcycle racing career.
He returned to the MotoGP grid in 2011 with LCR Honda but endured his worst premier-class season, scoring 61 points and finishing fifteenth in the championship. He returned to Moto2 in 2012 with Aspar before a brief stint filling in for the injured Hector Barbera at Pramac Ducati in MotoGP, racing the satellite GP12.
Elías transitioned to the MotoAmerica Superbike Championship in 2016 with Yoshimura Suzuki, immediately winning the first three races after being called in as a substitute. He finished third in the 2016 series with six wins, then dominated the 2017 season to claim the Superbike championship on ten victories and eighteen podium finishes, never finishing lower than second when he completed a race.
He finished runner-up in 2018 and 2019, both times behind champion Cameron Beaubier, then announced his retirement from MotoAmerica Superbike at the end of the 2020 season, having accumulated 32 career wins and 60 podium finishes in the series. He made a return to racing in subsequent years before abruptly announcing his retirement mid-season in 2023.
Elías is remembered for two things above all else: the extraordinary 0.002-second Estoril victory in 2006, which altered the course of that year's MotoGP title race, and his 2010 Moto2 title, which made him the first champion of a class that became the primary proving ground for future MotoGP stars. His success in MotoAmerica later in his career demonstrated a longevity unusual among riders who had made their name at the top level of Grand Prix racing.