And co-captain Jason King could be set for a stint on the sidelines after suffering a rib injury.
Watmough was put in the bad books after grabbing the arm of Kevin Locke and applying force in an attempt to roll the Warriors speedster onto his back.
Locke's arm twisted awkwardly during the movement, but the 23-year-old managed to play on.
Warriors five-eighth James Maloney was also placed on report for a high hit on Dean Whare, with the severity of the force knocking Whare's mouthguard out.
Manly centre Steve Matai delivered a similarly brutal hit on Locke earlier in the night, but the high contact was more accidental due to Locke slipping to the ground at the time.
The Sea Eagles' 11th win of the year lifted them to equal on points with fourth-placed Brisbane, but the Broncos can shoot two points clear with a win over last-placed Parramatta on Monday.
King was taken to hospital on Saturday night after coming off second best while attempting a tackle in the 16th minute.
The 31-year-old prop was cleared to fly back with the squad on Sunday, and will undergo further tests to determine the full extent of the damage.
Manly take on North Queensland in Townsville on Saturday night, with star fullback Brett Stewart a chance to return from a hamstring injury.
The Warriors were left ruing the one that got away after blowing leads of 18-0 and 22-6 against the Sea Eagles.
Manly halfback Daly Cherry-Evans was the hero, scoring a brace of tries in the final eight minutes to tie up the scores, before Jamie Lyon registered the match-winning conversion.
The Warriors' 11th loss of the season left last year's beaten grand finalists two points adrift of eighth spot, although that margin could stretch to four if Wests Tigers beat South Sydney on Sunday.
Warriors coach Brian McClennan conceded his side had no margin for error if they were to make the finals.
"I think we'll need to win our last five," McClennan said.
"But we've basically just stopped talking about trying to get to finals anyway. We've got to concentrate on one game at a time.
"We've got Cronulla next week and we're going to make sure we get it right."
A crowd of 20,095 watched the match at Patersons Stadium (formerly Subiaco Oval) in another boost to Perth's bid to snare an NRL team of their own.