The Movistar rider had led the general classification since the opening prologue, and held onto the lead throughout the next two days despite Jonathan Hivert winning stages one and two of the race.
Valverde then produced another winning display on the 183km third stage from Lucena to Rincon de la Victoria, keeping up with a lead group of 10 riders that was clear of the peloton entering the final descent, then beating Simon Spilak (Katusha) and Davide Rebellin (CCC Polsat Polkowice) to the line.
The stage win confirmed him as overall champion, with Jurgen van den Broeck (Lotto Belisol) coming second.
Hivert wins again at Ruta del Sol
"We couldn't have closed this race in a better way," said Valverde.
"In the finale, everyone was thinking of the stage win rather than the GC. The last turn was only 250 metres from the finish and I came in fourth place, maybe a bit too far, but I had good legs and could get to the top and win.
"I think that this is my best ever start for a season, and I'm the first one who is surprised about that. I cannot say I'm not well, because you can't win in bad form, but I wasn't expecting to do so well here.
"I'm lucky to live in Murcia and enjoy the good weather, so I can build a strong training base day by day and that makes gaining fitness easier.
"But the big goals are still far away and our plan is not to race too many competitions at this time of the year. I want to thank all team members, because they were splendid from the first to the last one - hats off."
Hivert wins first Ruta del Sol stage
Longo Borghini to donate prize money in support of women's cycling projects