Contador records 'extra special' win
The Tour de France champion won the final time trial eight seconds ahead of his closest rivals over the 12.4km course on the streets of Murcia.
Contador had struggled last month in his first race after being cleared of wrongdoing by the Spanish Cycling Federation, finishing fourth in the Volta ao Algarve.
"It was an amazing weekend, better than expected," the Saxo Bank-Sungard rider said.
"I had been eager to do well, because in Algarve, for various reasons, I was not up to standard, I could not concentrate on training, but I've been in Mallorca with the whole team and I am very happy with the outcome.
"Winning in Murcia is very important, because I had never won here before and because of what has happened in recent months, which have not been the best of my career. Winning here is extra special."
The three-times Tour de France winner tested positive for a small amount of the banned anabolic agent clenbuterol during last year's edition of cycling's most prestigious event.
The RFEC provisionally banned him for a year in August but reversed the decision last month.
Contador had denied deliberate wrongdoing, saying the failed test was due to contaminated meat.
His battle to clear his name may not be over, with cycling's world governing body still to decide whether to appeal against the RFEC decision.