The Catalan side doubled their lead in the 28th minute, Rakitic firing a superb volley in off the post after good work from Messi and Coutinho down Spurs' right.
The hosts were back in the game in the 65th minute, with Erik Lamela's shot from distance taking a deflection off Gerard Pique and sailing past Marc-Andre Ter Stegen. And I'm not saying that because he plays for my team.
"For 45 minutes, we didn't concede one chance to Messi - but of course when we are 2-0 down and you give more space as we are attacking", Pochettino said.
Rakitic stole the spotlight midway through the first half when the Croatia midfielder struck with a thunderous half-volley.
"We had a bit of bad luck while handling the game".
But Pochettino rejected the opinion that Messi had nearly single-handedly dismantled his team, adding: "We didn't concede one chance to Messi in the first half".
Messi has scored 10 goals in as many games this season, as well as providing five assists. And their job at Wembley was made no easier when Hugo Lloris came flying off his line in the second minute to make Philippe Coutinho's life a lot easier as he stroked the ball home from the edge of the box.
"We can't talk about topics, we need to talk about reality".
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And by "cash in", we mean "make a small percentage of their value from multi-billionaire team owners". He singled out the Dallas Cowboys as his preferred destination, but that did not happen.
Asked if Messi is the best player on the planet, he continued: 'Yes for me he is the best in the world.
"It was 4-2 of course for Barcelona but the team did everything and I feel so proud about their performance".
They have been rolling out the playing surface at Tottenham Hotspur's new stadium this week.
"I think for both teams the pitch wasn't great", said Pochettino. I'm always very happy when I see him'.
"It's so hard to stop this type of player". What can we do? "It's impossible to put it in better condition for today and Saturday of course".
Barcelona have six points to top the group as they lead Inter Milan on goal differential, while Tottenham have it all to do if they are to reach the last 16 having lost their opening two matches.
"If we start the game this way, it's so tough for the players". The goal galvanized the home side, who had some decent moments as they chased the game, but Messi put the result to bed in the 90th minute, capitalizing on a Tottenham giveaway. "We're still thinking the same, though, that all is possible".