In-form forward duo Neymar and Lionel Messi handed Luis Enrique's team a 2-0 first-half lead and there seemed little doubt that they would comfortably bounce back from a 3-2 loss at Paris Saint-Germain in the last round of Group F fixtures.
But Ajax stuck impressively to their task and substitute Anwar El Ghazi capitalised on growing anxiety in the Barcelona ranks to score in the 88th minute before Neymar's replacement Sandro secured victory with a fine counter-attacking goal.
"It was a good game because Ajax are a good team," Rakitic told Sky Sports.
"The work of the team was quite good so we have to do all the games like this.
"We hope that the next games will be the same."
Messi and the influential Andres Iniesta were also substituted before Ajax's late rally and it briefly appeared that Barca could pay the price for casting an eye towards Saturday's mouth-watering Clasico showdown with Real Madrid.
"These three players are unbelievable - they are so important for us," Rakitic said.
"It was a good game, also the last 20 minutes it was okay. It's normal that they can get a goal back.
"It was important that we got the third goal in the last minute. It was good work."
Edinson Cavani struck a late winner for Paris Saint-Germain at APOEL to deny Barcelona top spot in the group, although Rakitic insists he and his team-mates were unconcerned about events elsewhere, especially with the Ligue 1 champions facing a trip to Camp Nou in the final round-robin match.
"The most important thing is what we are doing," the Croatia international added. "We can't change what happens with Paris or the other teams.
"The most important thing today was three points, a good game and now we have to prepare the next game."
