The former Crystal Palace midfielder sustained the injury after a clash with Reds youngster Raheem Sterling in the first half.
Liverpool went on to to score three second-half goals, with Suárez netting a brace and Jose Enrique completing the victory.
The Wigan boss refused to attach blame to Sterling for Watson’s injury, although he was critical of an incident involving Suárez.
“I haven’t seen the challenge back, but I don’t think any of the players were looking at each other. Both were looking at the ball – it’s a real accident. It’s a nasty collision,” Martínez told BBC Sport.
“More of a disappointment was the stamp on Dave Jones by Luis Suárez. That was a challenge that he could have been punished for.”
He added: “It [Watson’s injury] is a broken leg and we will see the extent of the break and what treatment he needs.
“The injury affected us too much. We are really going to miss him. He has got a fracture.
“We are going to assess him now, maybe he needs surgery. It is too early to tell [how long he will be out for].
“We are really disappointed because Ben reached a really, really good level and today you could see that every time he got on the ball we were very penetrating with his quality.”
ENHANCED ODDS: Get 8/1 on Chelsea, Liverpool and City to win