Romelu Lukaku gave the European champions the lead shortly after the break in Abu Dhabi, before Raphael Veiga got their Brazilian opponents back on level terms from the penalty spot.
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Egyptian Captain and goalkeeper, Mohamed El Shenawy, was Al Ahly’s hero in the shootout, saving Felipe Melo’s penalty to ensure that the African champions won 3-2 in Qatar.
Scolari, who led Palmeiras to Brazil’s Serie A title last month, said he was mulling over the offer to replace Jose Pekerman.
Messi had been expected to feature in Ernesto Valverde’s starting lineup with Barca looking to extend their unbeaten record in La Liga to 28 matches
The 19-year-old agreed a five-year deal to join Pep Guardiola’s side in the summer but remained with Palmeiras until the end of the season