Leonardo Piepoli of Saunier-Duval crested the towering Colle S. Carlo with Basso, but the Smiling Assassin let Piepoli take all the risks on the descent to win Stage 13 by 44 seconds.
Meanwhile, challengers Jose Gutierrez (Phonak), Paolo Savoldelli (Discovery), Wladimir Belli (Selle Italia) and Gilberto Simoni (Saunier Duval) all lost at least between 30 seconds to more than 2 minutes to Basso.
The highlight of Saturday's 135-mile race between Alessandria to La Thuile was Colle S. Carlo, a 6.5 mile climb with an average grade of 10% that kicks up to 15% in places. While the races dealt with fog and drizzle in places, it was rain mixed with snow at the mountain top.
An early breakaway had a lead of up to 5 minutes early in the race, but the top riders' teams of Saunier-Duval (Simoni), Liquigas (Danilo Di Luca), Discovery (Savoldelli) and CSC (Basso) cut that to a minute by the base of the mountain.
The peloton broke up on the slopes of the Colle S. Carlo, with Basso finally riding clear of the last hangers-on, Simoni and Piepoli. However, Piepoli was able to cross the top with Basso, about a minute ahead of everyone else.
Tour de France hopeful Jan Ullrich, who looked so good winning the time trial two days ago, finished about 10 minutes behind the winner at the finish line.
1. Ivan Basso (Team CSC)
2. José E.Gutierrez Cataluna (Phonak), at 3:27 behind
3. Paolo Savoldelli (Discovery), at 5:30
4. Wladimir Belli (Colombia – Selle Italia), at 7:35
5. Gilberto Simoni (Saunier Duval), at 8:00
6. Franco Pellizotti (Liquigas-Bianchi), at 8:14
7. Tom Danielson (Discovery Channel), at 8:35
8. Damiano Cunego (Lampre), at 8:58
9. Danilo Di Luca (Liquigas-Bianchi), at 10:36
10. Victor Hugo Pena Grisales (Phonak), at 11:12.
More race details and updates are available at CyclingNews and VeloNews. OLN's website offers live video streaming of the Giro; OLN will broadcast Giro highlights from 5 to 7 p.m. (ET) Sunday (check local listings).
Sunday's Giro stage is a 138-mile route that tops two mountains, Gran San Bernardo and Passo Sempione with a finish in Domodossola.