The Argentina worldwide started on the bench and only came on for the final half hour in Barca's 2-0 victory over Sporting CP in their final Champions League group game on Tuesday and Rakitic stressed the importance of keeping the 30-year-old fresh.
Messi is believed to have a greater say in which transfer targets Barcelona try to sign after he penned a new lucrative four-and-a-half year contract to stay at Nou Camp.
The five-time Ballon d'Or victor has been in sensational form this season, scoring 17 goals in all competitions.
Rakitic said, "The truth is that he is happy, the important thing is that he is with us and that we have him on our side".
Pochettino says Spurs will learn from poor run
Despite Spurs' success in the Champions League thus far, the draw with Watford was their fourth Premier League match in a row without a victory, and they are a whopping 18 points off top spot.
"Sometimes he should rest".
Samuel Umtiti is set for two months on the sidelines while Javier Mascherano - who reportedly wants to leave the club - is also injured, leaving Thomas Vermaelen and Gerard Pique as the only fit central defenders.
December has just started and we know that Umtiti's injury is long-term but hopefully we can recover him in January. The 25-year-old had his heart set on a switch to the continent, but has knuckled down and still performed at his best levels for Jurgen Klopp's team despite his desire to leave.
"After so long it is clear I don't have much more to give to the club in the future", Mascherano told ESPN Deportes. "As a person and a player he's very important for the team".