It was a lacklustre first period from both sides with Alex Oxlade-Chamberlain and Messi having half-chances before Luis Suarez had two great chances to take the lead just before the break.
Neymar and Oliver Giroud both had a great opportunities at the beginning of the second period but failed to find the net, and Messi stepped up in the 71st minute to score the opening goal.
Suarez and Aaron Ramsey both missed from close range late on, but Messi's second from the spot made sure that Barcelona took an advantage back to the Nou Camp.
The atmosphere was fantastic inside the Emirates Stadium ahead of kick-off, but the excitement in the stands failed to materialise onto the pitch in what proved to be a pretty drab opening period.
The first bit of any real excitement didn’t arrive until the 16th minute when Andre Iniesta produced one of his classic balls towards the near post, however it was easy enough for Petr Cech. Dani Alves then had a try with the cross three minutes later but once again it was way too easy for Cech.
The first real chance at goal fell to the home side in the 22nd minute when Mesut Ozil set up Hector Bellerin. His blocked shot fell perfectly for Oxlade-Chamberlain, eight yards out but the lack of power on his shot made it easy for Marc-Andre ter Stegen.
Luis Enrique's side were presented with a great chance nine minutes from the break when Laurent Koscielny brought down Messi on the edge of the area. The Argentine tried to put under the wall, however the Gunners wall stood firm.
Enrique's side suddenly burst into life just before the break with star striker Suarez having two great chances to help his side take a lead into half-time.
The first literally came on the 45 minute mark, when the ball was slipped through to him by Messi. Instead of shooting, he attempted to unselfishly cut the ball back, and it was hacked clear.
The Uruguayan's second opportunity was even closer as the clock ran down in one minute of stoppage time. Alves volleyed back across goal from Sergio Busquets' pass, but Suarez flicked a header wide.
The Catalan side started the second period as they ended the first and Neymar had a great chance to open the scoring just four minutes after the restart. Iniesta played another brilliant ball into the Brazilian, and despite Messi waiting for the pass, Neymar went for it himself, only for Cech to block his shot.
After that early opportunity, Barca found themselves on the back foot and the Gunners had a great opportunity to take the lead for themselves.
Giroud's initial shot was blocked by Javier Mascherano, but the Frenchman was involved again almost instantly when he hit a low header that looked destined for the corner, only for Ter Stegen to somehow get a hand to it.
Despite being under the quash for the majority of the second period, it was Barcelona who took the lead 19 minutes from the end.
Their lead came from nothing, with a clearance from Gerad Pique falling to Neymar, who made a untracked run into the Gunners half and, unlike his earlier chance, laid it on a plate for Messi who made no mistake as he lifted the ball over Cech and into the net.
On a knifes edge
Despite Barca getting the crucial goal, the game was far from over as it entered the final 15 minutes, as Suarez had another great chance to get a goal.
It was another great move, this time spearheaded by Messi, who played it to Suarez after Neymar saw a shot blocked. The striker showed a great dummy to sit Cech down, only for his shot to come back off the post.
Substitute Danny Welbeck was causing problems when his looping header nearly fell for Ramsey, but the Welshman failed to get much on it as the ball rolled into the arms of ter Stegen.
Messi seals it
The game was all but sealed seven minutes from time when Messi added his, and Barcelona's, second of night.
He was gifted the opportunity when he latched upon Mertesacker's short pass, which caused Mathieu Flamini to trip the Argentine, leaving Cuneyt Cakir with no choice but to point to the spot. Messi had failed to score against Cech before this match, but no mistake as he sent the keeper the wrong way to secure the win, and his second against the ex-Chelsea 'keeper.
Neymar could have made it three right at the death when he got to a free header at the back post, but his soft effort was easy enough for Cech to push behind.