Vini Fantini-Selle Italia rider Chicchi shot up the inside of Guardini, next to the barriers, after the 11-times Langkawi stage winner opened his sprint too early.
Lithuanian Aidis Kruopis was third for Orica Greenedge on the 168km stage from Tapah to Kapar.
"I decided to watched Andrea and when he started sprinting with 300m to go I was on his wheel and could pass him," said Chicchi.
"This is my first time in Malaysia and at Tour de Langkawi. I'm very happy to be here because we came with a good team and we are successful."
GC leader Meiyin Wang finished 64th in the huge lead group of 126 riders.
Guardini, who left the previous incarnation of the winning team Farnese Vini for Astana in the winter, has been on the podium three times so far in this year's 10-stage race, but is yet to claim a stage.
"I'm used to winning all the sprints in this race but this year the competition is very high from Theo Bos to Francesco Chicchi and all the other good sprinters who are here," said Guardini.
"Today Francesco was better than me. He predicted the finish better than me. I was thinking of sprinting at 250m out but I started fifty metres earlier."
There was an early breakaway consisting of Yukiya Arashiro (Europcar), Taiji Nishitani (Aisan Racing) and Phuchong Sai-Udomsin (OCBC).
They went four minutes out before the peloton, led by Wang's small Chinese squad Xengxiang, began to close the gap. The time difference was two minutes with 30km to go, with the lead riders beginning to suffer in the heat. Arashiro broke away and would stay out the longest before being caught with 10km to go, with the main body of riders now controlled by the ProTour teams.
Bos (Blanco) seemed well-placed with two kilometres to go but would not ultimately threaten, while Guardini lived to regret beginning his push 300m from the line.