Anton, who grew up in a small village outside the Basque largest city, soloed to the most symbolic victory of his career after attacking from a small breakaway on the final climb of the day, 20km from the finish.
Cheered on by throngs of local Basque cycling fans all decked out in the eye-catchingly garish orange colours of the region's cycling team Euskaltel, Anton crossed the summit with a slender 30-second lead over Italy's Marzio Bruseghin (Movistar).
The 28-year-old Spaniard then produced the ride of his life to retain his advantage over the quick descent into Bilbao, crossing the line 41 seconds ahead of Bruseghin to send Spain's 10th biggest city into rapturous delight.
It was a historical moment for the cycling-mad Basque Country, which has not hosted a single stage of the Vuelta since 1978 following chaotic disruptions caused by stirring political tensions and pro-independence protests in the autonomous community of northern Spain.
There was no change in the general classification as both red jersey Juan Jose Cobo (Geox) and his nearest rival Chris Froome (Team Sky) finished safely in the pack around one-and-a-half minutes in arrears.
Anton was one of two Euskaltel riders who kept to the likely script and attacked 30km into the 158.5km stage from the Cantabrian coastal town of Noja.
Two other riders - Bruseghin and the Kazakh Alexsandr Dyachenko (Astana) - combined well with Anton and his team-mate Gorka Verdugo as the break built up a lead of six minutes over the first two Cat.3 climbs of the day.
Anton and Vergudo led the escapees over the summit of the Puerto de las Munecas and into the Basque County - but with the peloton starting to wake up, there was little time to savour the moment.
Combined work by Team Sky, Liquigas and Garmin-Cervelo saw the lead whittled down to just over four minutes as the quartet passed the famous Guggenheim museum in Bilbao for the first of numerous occasions in the closing 60km of the stage.
The lead was slashed to two-and-a-half minutes after the first of two crossings of the Cat.2 Alto del Vivero as Sky tried to pile on the pressure on the Geox team of red jersey Cobo.
Following the next descent, the leaders dropped the tiring Dyachenko as they passed through the animated streets of Bilbao once again.
An untimely puncture did for Verdugo's chances as temperatures rose to the high 30s.
Anton then made his move at the start of the final crossing of the Vivero climb, dropping Italian powerhouse Bruseghin with ease and using his superior climbing skills to increase his lead over the returning peloton to two minutes.
Back with the bunch, Bradley Wiggins was setting the pace for his Sky team-mate Froome who, 2km from the summit, launched a desperate attack to try and drop Cobo.
But the red jersey clung to Froome's wheel and the pair crossed the summit together before calling a truce and sitting up for the peloton.
By this time, Anton was riding himself towards the fourth Vuelta win of his career. Victory in his home town will act as a large consolation for Anton who, despite being tipped as one of the pre-race favourites, has had a difficult three weeks in Spain, dropping to 33rd in the GC more than 50 minutes off the summit.
Having shaken the hand of his directeur sportif in the closing straight, Anton kissed his Euskaltel shirt and crossed the finish line in a time of three hours 53 minutes and 34 seconds.
Bruseghin came home 41 seconds later, before German Dominik Nerz (Liquigas) led home a peloton containing both Cobo and Froome, 1:30 in arrears.
A tenth-place finish put young Dutchman (Bauke Mollema) within two points of the top of the green jersey standings, which is currently led by Katusha's Joaquim Rodriguez, who picked up points at the first bonus sprint but cracked on the final climb of the day.
French veteran David Moncoutie (Cofidis) retains the polka dot jersey as best climber. Moncoutie is seven points clear of the Italian Matteo Montaguti (Ag2R) with 28 points still available for the race's second day in the Basque Country.
The Vuelta continues on Saturday with the 185km stage 20 from Bilbao to Vitoria, which features four climbs including a tough Cat.1 ascent 45km from the finish.
With Britain's Froome still needing to make up 13 seconds if he wants to win the Vuelta, the stage will offer the last chance for Team Sky to put Cobo and Geox under pressure before the race concludes in Madrid on Sunday.