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Barca had temporarily been knocked off the summit following Real Madrid's 5-1 win over Tenerife earlier in the evening, but the champions reclaimed pole position after making it 11 wins from 12 league games at the Nou Camp this season.
Pep Guardiola's side, who have struggled for top form in recent weeks, had to bide their time to break down Malaga though despite dominating most of the match.
Pedro Rodriguez was the man to end the deadlock in the 69th minute but it would be Messi who was the match-winner with his 84th-minute tap-in coming after Malaga had shocked their hosts by drawing level through substitute Valmiro Valdo.
Malaga were the first to threaten when Duda tried to surprise Victor Valdes at his near post from a free-kick, which the Barca goalkeeper did well to keep out, but after that it was all one-way traffic towards the visitors' goal in the first half.
Barca fashioned a whole host of chances and half-chances, but a mixture of desperate defending, good goalkeeping and indifferent finishing meant the teams, incredibly, went into the break still on level terms.
Messi was a constant menace and might have had a first-half hat-trick, while a long-range Zlatan Ibrahimovic free-kick curled just wide and Sergio Busquets was unable to hit the target with his header when unchallenged six yards out.
Despite all Barca's supremacy though, visiting goalkeeper Gustavo Munua was not actually called into action on too many occasions before the break, although he produced a fine finger-tip save to keep out Xavi's clever flick from an Andres Iniesta cross.
The second half followed a similar script to the first, with Barca making most of the running.
Ibrahimovic saw his close-range header tipped over by Munua in the 51st minute when, not for the first time in the match, a Barca goal looked a certainty.
Moments later it was the head of centre-back Weligton that denied Barca as he cleared off the line after another Ibrahimovic header had looped over Munua.
Malaga were performing heroics in defence to keep Barca at bay, but they were finally breached in the 69th minute through Pedro.
A shot looked the last thing on the young winger's mind as he ventured in from the left wing, but he suddenly unleashed a snap-shot that flew inside the near post with Munua getting his hand to the ball but unable to keep it out.
At that stage it appeared Barca might go on to record a comfortable victory, and that might well have been the case if Iniesta's 76th-minute shot from Messi's quick free-kick had gone in instead of hitting the underside of the crossbar.
However, that stayed out and five minutes later the Catalan giants were stunned as Malaga drew level.
A quick one-two between Valdo and Victor Obinna put the former clean through on goal and the half-time replacement calmly slotted past Valdes before setting off to celebrate with his jubilant team-mates.
A shock was suddenly on the cards, but parity lasted just three minutes before Barca re-took the lead with a superbly-worked goal.
Xavi's fantastic pass put Dani Alves in on the right of the area, and the Brazilian instantly rolled the ball into the centre where Messi tapped home into an open net.
That was Messi's 17th league goal of the season, drawing him level with Valencia's David Villa at the top of the scoring charts, but more importantly it kept Barca at the top of the table.
Source: espnstar.com
