02-02-2012 -- Brazilian goalkeeper Diego Alves dived to his left to stop Messi's 56th-minute spot kick after Barcelona midfielder Thiago Alcantara had been fouled inside the area.
Valencia made a better start at their Mestalla stadium and scored first when Jeremy Mathieu sent a pass between Barcelona defenders for Jonas to rifle the ball into the top corner of the goal in the 27th.
The visitors equalised eight minutes later when Carles Puyol headed a corner past Diego Alves, who was caught out of position on Cesc Fabregas' inswinging cross.
Barcelona were lucky not to be reduced to 10 men when goalkeeper Jose Manuel Pinto raced to cut off Roberto Soldado and appeared to touch the ball outside of his area in the 18th minute.
The Spanish champions, who lost the domestic cup final to Real Madrid at the Mestalla in April, still hold the edge ahead of next Wednesday's return leg at the Camp Nou thanks to the away goal.
"That's the best thing, that we get to play in front of our fans with everything depending on ourselves," Barcelona midfielder Javier Mascherano said.
Messi had some early chances but, led by Pablo Piatti, Valencia exerted better control before Soldado volleyed over the bar in the 21st. A minute later, Barcelona striker Alexis Sanchez rushed a shot on his wrong foot after a breakaway.
Valencia's best scoring opportunities originated from the left, with Jordi Alba sending Mathieu flying down the flank and the France winger passing perfectly between Puyol and Gerard Pique for Jonas to redirect the ball into the net.
Diego Alves did well to deny Sanchez after Isaac Cuenca's impressive dribble had given the Chile international a great chance, and Barcelona capitalised on the ensuing corner as Puyol caught the goalkeeper wandering to score his third goal of the season.
Valencia fullback Miguel Brito gave away the spot kick, but Diego Alves refused to dive early to ensure Messi had a second penalty saved this season.
"You have to be patient. I'm just glad I could help the team," Alves said.
Barcelona finally found their groove to have the better opportunities late on. Pique headed Messi's flicked-on cross over and substitute Daniel Alves went close on several occasions especially a cross-goal shot that came off the far post in the 73rd.
Messi, who has looked fatigued recently, pulled a stoppage-time attempt wide of the near post to end the match.
Barcelona coach Pep Guardiola accepted the European champions were lucky to escape with the draw, while Valencia's players were upset with the referee in a week in which their opponents have expressed their unhappiness with the officiating this season.
Soldado, whose team received six bookings to Barcelona's two was vented out his frustration after the match.
"He clearly saw (Pinto handle) but he didn't want to call it," said Soldado, whose team received six bookings to Barcelona's two. "(But) we're not going to give up. The tie is in their favor now, 60 percent to them and 40 percent to us."
Athletic Bilbao leads third-tier club Mirandes 2-1 in the other semi-final. The return leg is at San Mames on Tuesday.