The Brazilian shared pictures of the Blues' FA Cup victory on Instagram, but seems to have completely obscured Conte with cup emojis.
There are already rumours of a rift between the player and his Italian manager - and Conte's future at the club remains unclear.
Willian came off the bench in the 91st minute of Saturday's FA Cup final against Manchester United at Wembley, which the Blues won 1-0.
The 29-year-old made 36 Premier League appearances this season, 16 as a substitute.
He has since deleted the post, but not before it was screengrabbed and shared on social media.
Source: BBC NEWS