The expected winners of the stage were so preoccupied managing themselves that they allowed Alaphilippe and Max Richeze to open up a gap going into the final 200m.
The sprinters realised their mistake, but too late, with even Deceuninck – Quick-Step's own Elia Viviani not able to pip Alaphilippe on the line.
Watch the remarkable finish as Alaphilippe beats the sprinters to Stage 6 win
"It’s been a successful week for Deceuninck – Quick-Step here in Italy and I am glad I could finish off the squad’s amazing work today," said the Frenchman after his stage win. "Kasper, Yves Max, everybody contributed to the pace and did a magnificent job on this stage, and for that I am extremely grateful.
"During the stage, Elia told me it was going to be a hard sprint and that he didn’t feel that good, so I was free to try and go for it. Everybody was tired today, you could see that in the bunch. I told him that we will see, then in the last kilometer I found myself on Max’s wheel and as soon as he dropped me in the front, I went full gas and that was it.
"I can’t tell you how happy and proud I am of my team, whom I want to thank, because this is also their victory."
Adam Yates protected his overall lead, which stands at 25 seconds over Primož Roglič, and speaking after the stage he said:
Like I said yesterday and like I said from the beginning, I’ll do my best and if it’s not good enough, it’s not good enough. I came here to win stages and I didn’t manage to win a stage but I got close on a couple of occasions and we’ve held the jersey for a few days now.
“So in my mind it’s been a good race, a good race for the team and whether or not I can hold on tomorrow, we’ll find out won’t we?”
Stage Six Results
1. Julian Alaphilippe (Fra) Deceuninck – Quick-Step, in 4-42-11
2. Davide Cimolai (Ita) Israel Cycling Academy
3. Elia Viviani (Ita) Deceuninck – Quick-Step
4. Clement Venturini (Fra) Ag2r La Mondiale
5. Peter Sagan (Svk) Bora-Hansgrohe
6. Maximiliano Richeze (Arg) Deceuninck – Quick-Step
7. Jens Keukeleire (Bel) Lotto-Soudal
8. Greg Van Avermaet (Bel) CCC Team
9. Reinardt Janse van Rensburg (RSA) Dimension Data
10. Simone Consonni (Ita) UAE Team Emirates, all at same time
1. Adam Yates (GBr) Mitchelton-Scott, in 25-15-59
2. Primož Roglič (Slo) Jumbo-Visma, at 25 seconds
3. Jakob Fuglsang (Den) Astana Pro Team, at 35s
4. Tom Dumoulin (Ned) Team Sunweb, at 1-55
5. Julian Alaphilippe (Fra) Deceuninck – Quick-Step, at 2-34
6. Wout Poels (Ned) Team Sky, at 2-39
7. Thibaut Pinot (Fra) Groupama-FDJ, at 2-46
8. Sam Oomen (Ned) Team Sunweb, at 2-58
9. Simon Clarke (Aus) EF Education First, at 3-03
10. Rui Costa (Por) UAE Team Emirates, at 3-26