Basso, in an A-Style M-Sport Ford Fiesta RRC, was 3.8s quicker than Mikkelsen through the second run of the 19.33-kilometre Sestino stage.
He said: “Everything’s okay, it was clean and there was no dust. I am much happier.”
Mikkelsen, the reigning Intercontinental Rally Challenge champion, reported an upturn in confidence due to the cleaner nature of the tricky gravel roads.
However, he said he was now struggling to match the pace of Basso’s turbocharged Fiesta in his normally-aspirated ŠKODA Fabia Super 2000.
“It’s much better now it’s cleaner,” said Mikkelsen. “Basso is doing a very good job and I am losing time in the uphill hairpins against the turbo car.
“I am not pushing to the maximum because the stages are tricky and I have to be careful. Maybe tomorrow.”
Despite slipping from first to fourth overall, Sepp Wiegand said he could not be disappointed: “For me it’s okay, I was happy with the stage.
“ I am very young and I don’t have so much experience. Maybe the soft tyres were not the best choice for this stage.”
Umberto Scandola said the power loss issue that affected him this morning was still hampering his pace.
However, he remains firmly in contention for victory, 3.3s behind Mikkelsen after going third fastest in his Fabia.
Heading to the fourth stage of the event, the top four drivers are covered by 4.4s, which underlines the competitive nature of the IRC.
Meanwhile, Japan’s Toshi Arai has been forced to retire after a ball joint failed on his Subaru Impreza R4 STI on the road section heading to stage four.
The vastly experienced Arai and Australian co-driver Dale Moscatt were in second place in the IRC Production Cup, 34.7s behind Tommi Makinen Racing team-mates Jarkko Nikara and Jarkko Kalliolepo.
They were 150 metres from the stop line of stage three when they were forced out.
Arai and Moscatt are the defending IRC Production Cup champions. Rally San Marino is their second appearance of 2012 and it is not clear if they will be able to restart on day two.