Arsenal went ahead at the Nou Camp through Nicklas Bendtner early on to take the lead in the tie for the first time, but the Gunners' joy was short-lived as Messi struck a brilliant first half hat-trick, before compounding the Londoners' misery with a fourth late on as Barca won 4-1 on the night, 6-3 on aggregate.
Wenger likened Barca's brilliant Argentinian winger to a computer creation.
"He's like a PlayStation," the Arsenal coach said after the match, when asked to describe the Argentinian's performance.
"I think he can take advantage of every mistake you make. Barcelona are a very good side but of course they have Messi who can make the difference at any moment in the game," he said.
Wenger believes the 22 year-old can go on to become one of the great players of all-time.
"He is very young but he can achieve a lot - there are not many players who can score four goals like he did.
"He has six or seven great years ahead of him and he can become unbelievable - touch wood nothing happens to him," he said.
Wenger was upbeat despite Arsenal's quarter-final exit, but the Frenchman is concerned this result will have a detrimental effect on his side's Barclays Premier League title aspirations.
"Of course you worry because it's a big disappointment - we have to recover quickly to fight for the Premier League, and focus completely now on that," he said.
"It seems a very empty future (after a defeat like this). It's a big disappointment but we have to ready for the next game," he said.
Arsenal's next match is a trip to White Hart Lane for the north London derby next Wednesday and Wenger believes the prospect of facing local rivals Tottenham could give his players the lift they need following tonight's defeat.
"It's a place where we have done well (in the past) and it forces you to focus straight away because it's a derby," he said.
Wenger was missing a host of players through injury for tonight's match and admitted he would like to have been able to select captain Cesc Fabregas.
"It's difficult to know how much we missed Fabregas, tonight we missed seven or eight players, but if you had asked me before the game, of course I would love to have had Fabregas," he said.
The Gunners led for less than three minutes on the night, but Abou Diaby missed a great opportunity to set up Theo Walcott for a possible second goal when they were one up, and Wenger believes that was a key moment.
"We had a good opportunity to score the second goal. Before they equalised, we had a great chance to score again, but we made a very bad decision with the final ball and they came back straight away," he said.
"So there are regrets because we started well, but we made too many mistakes defensively and we were punished," he said.
Nevertheless, the Arsenal coach said he was proud of his young players and believes the club has a great future as the likes of Walcott, Bendtner, (Samir) Nasri and Diaby mature in the next few years.
"We had a very young team tonight and that is very positive - we had six or seven players under 23 in the team and they did well.
"Where we lacked maturity was in the final ball, but players like Walcott, Bendtner, Nasri and Diaby are all very young - they are showing great qualities every year and they will only get better," he said.
Wenger did admit that some changes will be necessary in the summer, but says he will take some time to reflect on what is required.
"We have to add something for sure, but we have some time to think about that," he said.