The Argentina superstar scored Barca's second with a gorgeous 20-yard finish after a swift breakaway in the 12th minute, but he fell awkwardly soon after in a coming together with Sevilla's Franco Vazquez.
Writhing in pain on the field, Messi was tended to by team trainers before being substituted off for Ousmane Dembele.
However, Rakitic restored Barca's three-goal advantage with a superb volley that sailed into the bottom corner. After the game the defender said: "It was an important match against a Sevilla who arrived as leaders and we knew that we had to win to put ourselves there".
"There's a big difference between having him on the pitch or not but we have a strong enough team to win games whether he plays or not".
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Ernesto Valverde, and Barça fans around the globe, will be keeping their fingers crossed ahead of the Champions League match on Wednesday and then the clash against their bitter rivals, Real Madrid. "We will be prepared to overcome this".
"We have to prepare ourselves, it is clear we are going to notice the loss of Messi but we have players that can cover".
And before the quarter of the hour mark he got himself on the scoresheet to double Barca's lead.
Barcelona were able to see out the game against Sevilla with a 4-2 victory, but the atmosphere remained subdued due to the uncertainty over Messi.
"He gives us a lot of peace of mind when he is around but we don't have to suffer without him", he said. "We will try to maintain our style".