Missaglia, a member of the overall leader Pavel Tonkov's Mapei team, completed the route of 159km (98.6 miles), starting and finishing at Lido di Camaiore, in 3hr 36min 24sec.
He edged out fellow Italians Andrea Vatteroni, Mirko Celestino and Massimo Podenzana for the victory, while the main pack of riders came in about one minute behind. Tonkov, the 1996 Giro champion, retained his 41-second advantage over France's Luc Leblanc.
"It's a great day for me. Everything went as well as it could have. When there were just four of us, the others tried to pull away from me, but as you could see I was able to stay there and win," Missaglia said.
Italy's Stefano Casagranda fell when a food sack got caught in the spokes of his bicycle. He appeared to have lost consciousness momentarily, and was taken to hospital.
Before the stage, France's Thierry Laurent, Ukraine's Vladimir Poulnikov and Italy's Marco Gili and Roberto Moretti were banned from the Giro when tests revealed red blood cell counts that were too high, officials said. The International Cycling Union said the riders can not compete for 15 days because they are not medically fit.
The pre-race tests were introduced by the ICU earlier this year, and yesterday's action brings to 10 the number of riders ruled out by the new procedure. Excessive levels of red blood cells can be a sign of use of EPO (Erythropoietin), a banned substance which is undetectable in standard urine tests. The higher count can also occur naturally.
The Giro continues today with the 212km stage from Varazze to La Spezia.
Results, Digest, page 30