It was a near faultless performance from the Argentine but Pochettino was happy with how Spurs dealt with him in the first half although conceded he was hard to stop as the game developed.
Coutinho performed a minor miracle to keep the ball in play on the byline with Rakitic launching himself into a sensational 20-yard volley that clipped the post on its way into Lloris' net. This was the sort of majestic performance which first established Messi as the world's best and showed that he is still at the top of his game all these years later. Spurs could not get near him and he left the watching crowd gasping twice within the space of five minutes as two nearly identical efforts struck the same portion of Lloris's right-hand post.
Everybody who will play the game in the future will also be struggling to match him.
Messi's second goal was a stunner, which epitomised his performance, with the Argentine stroking the ball home at the near post after neat build-up play by Coutinho and Luis Suarez.
Spellbound by Messi's magic, Tottenham backed off again moments later as the striker hit the woodwork for a second time.
Barcelona were vulnerable so they said, but on a pitch scarred from hosting British heavyweight champion Anthony Joshua's fight against Alexander Povetkin they took only two minutes to catch Spurs in the solar plexus.
But question marks do remain about their ability to seriously challenge for the Champions League title this season, despite making it two wins from two to open up group play. Sure, they missed the pace and dominant aerial ability of the suspended Samuel Umtiti as Harry Kane in particular bullied their back line in the second half. If you watch the game, in the first half - how many chances did Messi have?
The visitors, returning to Wembley for the first time since lifting the Champions League there in 2011, extended their lead in stunning fashion soon after Kane had Spurs' first shot.
Tottenham have collected zero points from their opening two Champions League fixtures this season, with Barca and Inter both on six.
'With respect to the other players, Messi is unique, ' he added.
Spurs twice rallied, making it 2-1 and then 3-2 and almost equalising with a deflected Lucas Moura effort, but Lionel Messi's 90th-minute strike - his second goal of the night - ended Spurs' hopes.
But the damage was done due to defensive errors from Lloris and Sanchez as they badly missed Vertonghen's calming influence and Dembele's presence in front of the back four.