Stewart managed to stay on his bike but was forced to stop pedalling and finished the race in 29th place, as Elia Viviani (Cofidis) took the victory in the one day event.
Following an exchange between the two after the finish, Stewart took to Twitter to lambast Bouhanni for his behaviour, attaching footage of the incident.
"I would ask you what you was thinking... but you clearly have no brain cells," Stewart wrote.
"The ironic thing is, you told me I had 'no respect' after the finish. Here's an educational video of what 'no respect' looks like."
The UCI announced on Monday that it had referred the incident to its Disciplinary commission, as further repercussions loom for Bouhanni.
"The UCI firmly condemns the dangerous conduct of the rider Nacer Bouhanni," a statement said, adding that the UCI will "demand the imposition of sanctions that are appropriate to the seriousness of this action."
The incident drew similarities to when Bouhanni deviated from his line at both Paris-Nice and the Hamburg Classic in 2016, for which he was also relegated.