He edged Pello Bilbao (Bahrain McLaren) with Brandon McNulty (UAE Team Emirates) leading the pursuers in, one second behind.
Dylan Teuns (Bahrain McLaren) and Jack Haig (Mitchelton-Scott) were gapped inside of 50m to go, when the pair at the front inexplicably took the race vehicle caravan exit, costing them precious seconds.
Fuglsang remains in command of the general classification, ahead of the Bahrain trio of Mikel Landa, Bilbao and Teuns.
Landa is 14 seconds behind in second. Bilbao is 30 seconds adrift in third. Teuns is a further second behind in fourth.
On Saturday, the fourth and penultimate stage will take riders over 126 km between Villaneuva Mesia and Granada, before the decisive fifth and final stage, a 13km individual time trial around Mijas on Sunday.
Vuelta a Andalucia 2020 – stage 3 results (Jáen – Ubeda):
| 1 | Jakob Fuglsang (Astana) | 4:33:25 |
| 2 | Pello Bilbao (Bahrain McLaren) | ,, |
| 3 | Brandon McNulty (UAE Team Emirates) | +01” |
| 4 | Ion Izagirre (Astana) | +04” |
| 5 | Marc Soler (Movistar) | +06” |
| 6 | Dylan Teuns (Bahrain McLaren) | +08” |
| 7 | Jack Haig (Mitchelton-Scott) | ,, |
| 8 | Mikel Landa (Bahrain McLaren) | ,, |
| 9 | Antwan Tolhoek (Jumbo-Visma) | +13” |
| 10 | Maurits Lammertink (Circus-Wanty Gobert) | +26” |
Vuelta a Andalucia 2020 – general classification after stage 3:
| 1 | Jakob Fuglsang (Astana) | 14:22:26 |
| 2 | Mikel Landa (Bahrain McLaren) | +14” |
| 3 | Pello Bilbao (Bahrain McLaren) | +30” |
| 4 | Dylan Teuns (Bahrain McLaren) | +31” |
| 5 | Ion Izagirre (Astana) | +34” |
| 6 | Jack Haig (Mitchelton-Scott) | +35” |
| 7 | Chris Harper (Jumbo-Visma) | +01’23” |
| 8 | Marc Soler (Movistar) | +01’27” |
| 9 | Ruben Fernandez (Fundacion-Orbea) | +01’36” |
| 10 | Harm Vanhoucke (Lotto Soudal) | ,, |
