The 28-year-old is now 16th in the overall rankings, 16 seconds behind new leader Yates.
There were also second round wins for fourth seed Stefanos Tsitsipas of Greece, fifth seed Alexander Zverev of Germany and seventh seed David Goffin of Belgium.
"I didn't realize at all that it was unauthorized," Alaphilippe said, "But if that's how it is, then no worries. I'll pick myself up again and we'll forget about it."
In women's singles, top seed Pliskova of the Czech Republic was upset by France's Caroline Garcia in the second round.
The women's pole vault event was also won by a Swede, as Angelica Bengtsson finished with a best jump of 4.72 meters. Enditem
In the 65th minute, Dalian's Ke Zhao added a goal of his own and sealed the 4-0 victory.
Fiorentina loanee Pedro put the visitors ahead in just the second minute by pouncing on an errant pass and sliding home from close range.
The 31-year-old's poor relationship with Real Madrid coach Zinedine Zidane is well documented and was made clear when Zidane only used him in two of the 12 games his side played when Spanish football resumed in June after lockdown.
Duplantis tried to challenge Sergei Bubka's 26-year-old outdoor record of 6.14 meters, but failed to continue after one unsuccessful attempt at 6.15 meters as darkness set in.
"It was a heavy finish. It was maybe the most easy stage I ever did in a cycling race because there was no breakaway, not a high pace at all, but then the last hour was really hectic with the wind," Van Aert said.
"It was a fantastic evening. The conditions, crowd, competition - it was all fabulous. Sam is a fabulous competitor, and I feel we bring the best out of each other," Duplantis added.