Ewan claimed his first Grand Tour stage victory by beating John Degenkolb and Peter Sagan in a sprint at the end of the 167.3km Rota-Alcala route.
Giant-Alpecin's Dumoulin finished two seconds later in a pack for a one-second advantage over Esteban Chaves.
Britain's Chris Froome was 12th and is 35 seconds behind overall.
The Team Sky rider is aiming to become the third rider to win the Tour de France and the Vuelta in the same year.
Spaniard Alejandro Valverde, who started as one of the favourites for the title, dropped to fifth overall, 29 seconds adrift of Dumoulin.
Stage five result:
1.  Caleb Ewan (Aus/Orica)- three hours, 57 minutes and 28 seconds
2.  John Degenkolb (Ger/Giant) Same time
3.  Peter Sagan (Svk/Tinkoff - Saxo) Same time
4.  Jempy Druecker (Lux/BMC Racing) Same time
5.  Jose Joaquin Rojas (Spa/Movistar) +2secs
6.  Kristian Sbaragli (Ita/Team MTN) +2secs
7.  Domenico Pozzovivo (Ita/AG2R) +2secs
8.  Daniel Moreno (Spa/Katusha) +2secs
9.  Tosh Van der Sande (Bel/Lotto) +2secs
10. Nikolas Maes (Bel/Etixx - Quick-Step) +2secs
11. Tom Van Asbroeck (Bel/LottoNL) +2secs
12. Chris Froome (GB/Team Sky) +2secs
15. Tom Dumoulin (Ned)/Giant) +2secs
General classification after stage five:
1.  Tom Dumoulin (Ned/Giant) 17 hours, nine minutes, six seconds
2.  Esteban Chaves (Col/Orica) +1sec
3.  Nicolas Roche (Ire/Team Sky) +16secs
4.  Daniel Martin (Ire/Cannondale) +25secs
5.  Alejandro Valverde (Spa/Movistar) +29secs
6.  Daniel Moreno (Spa/Katusha) +31secs
7.  Chris Froome (GB/Team Sky) +35 secs
8.  Joaquim Rodriguez (Spa/Katusha) +36secs
9.  Nairo Quintana (Col/Movistar) +37secs
10. Fabio Aru (Ita/Astana) +48secs
Tom Dumoulin of the Netherlands became the new Vuelta a Espana leader after Wednesday's fifth stage, won by Australian Caleb Ewan.