Messi was felled by a badly timed challenge from Atletico Madrid defender Tomas Ujfalusi that damaged ligaments in his right ankle. He will miss Barca's La Liga match at home to Sporting Gijon on Wednesday and Saturday's trip to Athletic Bilbao and may be out for longer.
Real coach Jose Mourinho suggested recently that players are targeting Ronaldo's troublesome ankle, while Messi's Barca team-mate Gerard Pique accused opponents of "hunting" the World Player of the Year.
"Right now it seems that anything goes in the world of football and that saddens me," Pique said on Spanish radio.
The challenge by Ujfalusi in added time at the Calderon, which led to the Czech being shown a straight red card, had been "very ugly" and could have put Messi out of action for a long time, Barca captain Carles Puyol told reporters.
"We have to stamp these things out but the referee did his job by showing the red card," the Spain defender said.
"People are always talking about how we need to protect this or that player but you have to protect everyone."
Barca's 2-1 win over Atletico put their bid for a third straight La Liga triumph back on track after the previous weekend's shock 2-0 home defeat to promoted Hercules.
Coach Pep Guardiola rested key players for that match with an eye on midweek Champions League action but fielded his strongest team on Sunday.
Atletico were unable to cope with the champions' fast-flowing play and customary domination of possession and the 2-1 scoreline flattered the hosts.
HIGH HOPES
With three matches played, Valencia are the only team to have a perfect nine points, with Barca's arch rivals Real, who won 2-1 at promoted Real Sociedad on Saturday, on seven, level with Sevilla. Barca are on six along with Atletico, Villarreal and Espanyol.
Real can stretch their lead over Barca to four points with a win at home to Espanyol on Tuesday. Atletico play at Valencia on Wednesday and Sevilla host Racing Santander on Thursday.
Hopes are high at Real, who have spent around 350 million euros on players and coaching staff since Florentino Perez returned to the presidency last year, that they now have what it takes to topple Barca, according to midfielder Esteban Granero.
"We have started the league well and we have to continue on the same path," he said at a news conference on Sunday.
"We are convinced in the dressing room that this year we can and must be ahead of Barcelona."
