Messi was rested by Barca head coach Ernesto Valverde in Tuesday's 2-0 win over Sporting CP, with qualification for the Champions League last 16 already secured, and Croatia global Rakitic stressed the importance of keeping the 30-year-old fresh.
Meanwhile, Rakitic hopes Messi's countryman and Argentina team-mate Javier Mascherano, 33, stays at the Nou Camp.
"I think that my stage here is ending", Mascherano said.
"It's good that he was good in this game and we have to look after him well".
The five-time Ballon d'Or victor has been in sensational form this season, scoring 17 goals in all competitions.
"I don't say that with a heavy heart, it is the opposite".
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However, he doesn't believe the success will continue in a few years time, with much of Barcelona's successful core of players reaching towards twilight of their careers.
Valverde said: "We have time to analyse that decision. We know Sam's injury is a long one but he will return in January", added Valverde.
"These questions emerge when there are injuries, there's always talk but, in principle, we're happy with the centre-backs we have got".
Barca are already assured of their place in the Champions League last 16 as Group D winners, meaning Valverde is likely to heavily rotate his side for Sporting's visit to the Camp Nou.
The central-midfielder-turned-centre-back was still at boyhood club River Plate at the time when Real raised their interest in his services, but he moved to Brazilian outfit Corinthians in 2005 and West Ham United a year later. "We know we have to look for solutions".