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On a day of mixed fortunes for the host nation, local overall favourite Igor Anton cracked halfway up the 23km final climb and lost 87 seconds on the other contenders.
Katusha rider Moreno had no such problems on another day of intense heat, blasting away from Denmark's Chris Sorensen with 200m to go for the first Grand Tour stage win and 10th victory of his career. Ireland's Dan Martin was third.
Moreno told reporters he had spoken to team-mate and leader Joaquin Rodriguez who told him to take his chances.
"When we got to the last km and I looked back and saw how fast the rest of the favourites were coming up, then I thought we wouldn't make it," Moreno said.
"But I hung on and hung on and I knew if it came down to a two-way fight against Sorensen, I'd win."
Chavanel said taking the Tour of Spain lead on such a gruelling day confirmed he had bounced back from a difficult Tour de France.
"I'm very motivated for this race and the last part of the season," said Chavanel, who suffered a painful shoulder injury in the first week of the Tour de France.
"I could only get second in yesterday's stage, but I knew if I held on at the bottom of the Sierra Nevada climb, where it was steepest, I'd have a chance today to lead.
"I led this race in 2008 for a day, too, and I'm as determined now as I was then to defend it as hard as I can."
After the race's first major mountain top finish, Chavanel leads by 43 seconds over Moreno while Dane Jakob Fuglsang is third at 49 seconds.
Briton Mark Cavendish abandoned the race.
"We don't know what was wrong him, he's just totally out of energy, no power at all" Cavendish's sports director Jens Zemke said. "He told me he was so tired he felt like he could fall asleep the minute he got into the team car."
The race finishes in Madrid on September 11.
Results of the fourth stage of the Tour of Spain, a 170.2km ride from Baza to Sierra Nevada on Tuesday:
1. Daniel Moreno (ESP/KAT) 4hr 51min 53sec
2. Chris Anker Srensen (DEN/SAX) at 0:03sec
3. Daniel Martin (IRL/GRM) 0:11.
4. Joaquin Rodriguez (ESP/KAT) 0:11.
5. Przemyslaw Niemiec (POL/LAM) 0:11.
6. Serguey Lagutin (UZB/VAC) 0:11.
7. Jurgen Van den Broeck (BEL/OLO) 0:11.
8. Wout Poels (NED/VAC) 0:11.
9. Michele Scarponi (ITA/LAM) 0:11.
10. Bauke Mollema (NED/RAB) 0:11.
11. Kanstantsin Siutsou (BLR/HTC) 0:11.
12. Vincenzo Nibali (ITA/LIQ) 0:11.
13. Mikel Nieve (ESP/EUS) 0:11.
14. Janez Brajkovic (SLO/RSH) 0:11.
15. Haimar Zubeldia (ESP/RSH) 0:11.
16. Denis Menchov (RUS/GEO) 0:11.
17. Steven Kruijswijk (NED/RAB) 0:11.
18. Bradley Wiggins (GBR/SKY) 0:11.
19. Fredrik Kessiakoff (SWE/AST) 0:11.
20. Luis Leon Sanchez (ESP/RAB) 0:11.
Overall standings:
1. Sylvain Chavanel (FRA/QST) 13hr 19min 09sec
2. Daniel Moreno (ESP/KAT) at 0:43sec
3. Jakob Diemer Fuglsang (DEN/LEO) 0:49.
4. Maxime Monfort (BEL/LEO) 0:49.
5. Vincenzo Nibali (ITA/LIQ) 0:53.
6. Kanstantsin Siutsou (BLR/HTC) 0:58.
7. Fredrik Kessiakoff (SWE/AST) 0:59.
8. Sergio Pardilla (ESP/MOV) 1min 03sec
9. Marzio Bruseghin (ITA/MOV) 1:03.
10. Kevin Seeldraeyers (BEL/QST) 1:04.
11. Daniel Martin (IRL/GRM) 1:06.
12. Jurgen Van den Broeck (BEL/OLO) 1:07.
13. Joaquin Rodriguez (ESP/KAT) 1:14.
14. Mikel Nieve (ESP/EUS) 1:17.
15. Janez Brajkovic (SLO/RSH) 1:18.
16. Haimar Zubeldia (ESP/RSH) 1:18.
17. Bauke Mollema (NED/RAB) 1:19.
18. Luis Leon Sanchez (ESP/RAB) 1:19.
19. Michele Scarponi (ITA/LAM) 1:21.
20. Chris Froome (GBR/SKY) 1:31.
