The Sardinian climber would have been far from expected to make any kind of influence on the stage outcome at the start of the day, with a relatively sedate 187km course that featured the tricky Côte de Sécheras climb with 20km to go.
And that’s where much of the action happened, with Tony Martin (Etixx-Quick Step) attacking on the climb to go solo, with Aru then instigating a move which saw a number of riders including Adam Yates (Orica-GreenEdge) and Mikel Landa (Team Sky) form part of a large leading group which pulled back Martin.
The sprinters’ teams then worked hard to try and pull them back with a gap of only eight seconds, but Aru took his chance with 12km remaining to put some distance into those behind as his companions were pulled back.
The 2015 Vuelta a España winner didn’t gain much more than 10 seconds on the long descent towards the finish, with peloton constantly hovering just behind him.
His advantage came on the tight and twisting corners though, taking a fast line through some dangerous looking curves that peloton were forced to slow up for.
Race leader Alberto Contador (Tinkoff) appeared to lose contact with the bunch on a tough bridge crossing on the descent before chasing back on, while Tony Martin went down on a corner further up the descent.
As Aru hit the final flat run in towards the finish Tournon-sur-Rhône it became apparent he could just hold on despite the work of Nacer Bouhanni (Cofidis) and Alexander Kristoff’s (Katusha) teammates, putting a huge final effort to hold the sprinters off and cross the line in celebration just two seconds ahead.
The day’s main break, consisting of Niki Terpstra (Etixx-Quick Step), Thomas De Gendt (Lotto-Soudal) and Dimitri Claeys (Wanty Groupe-Gobert) got away very early on and built a maximum gap of almost six minutes.
That gap crept down thanks to the work of Cofidis and Katusha, and Cyril Gautier (Ag2r La Mondiale) and Perrig Quémeneur (Direct Energie) took the chance to jump across to those riders out front.
Gautier managed to stick on to the front three as Quémeneur lost contact, but they were eventually caught by the peloton before the final category two climb of Côte de Sécheras with 26km to go.
It was then Aru who the lit up the race to take the stage win, and may be looking for further success in the remaining stages with a 1-15 deficit already on GC.
Thursday’s stage four sees the riders take on a 176km course from Tain-l’Hermitage to Belley, which might prove the last chance for the sprinters before the race heads towards the bigger climbs.
Critérium du Dauphiné 2016, Boën-sur-Lignon to Tournon-sur-Rhône (187.5km)
1. Fabio Aru (Ita) Astana, in 4-19-54
2. Alexander Kristoff (Nor) Katusha
3. Niccolo Bonifazio (Ita) Trek-Segafredo
4. Julian Alaphilippe (Fra) Etixx-Quick Step
5. Edvald Boasson Hagen (Nor) Dimension Data
6. Sam Bennett (Irl) Bora-Argon 18
7. Daryl Impey (RSA) Orica-GreenEdge
8. Nacer Bouhanni (Fra) Cofidis
9. Enrico Gasparotto (Ita) Wanty-Groupe Gobert
10. Arthur Vichot (Fra) FDJ, all at 2s
Overall standings after stage three
1. Alberto Contador (Esp) Tinkoff, in 13-13-10
2. Richie Porte (Aus) BMC Racing, at 6s
3. Chris Froome (GBr) Team Sky, at 13s
4. Daniel Martin (Irl) Etixx-Quick Step, at 21s
5. Julian Alaphilippe (Fra) Etixx-Quick Step, at 24s
6. Jesus Herrada (Esp) Movistar, at 27s
7. Adam Yates (GBr) Orica-GreenEdge, at 31s
8. Diego Rosa (Ita) Astana, at 37s
9. Daniel Navarro (Esp) Cofidis, at 43s
10. Bauke Mollema (Ned) Trek-Segafredo, at 44s