"We watched an incredible game of football and I can't say if the draw is fair or not", said Real coach Zinedine Zidane, who would not be drawn on the referee's performance.
Sergi Roberto had just been sent off for a clash with Marcelo when Messi made a beeline for Hernandez.
Barca opened the scoring through Luis Suarez, only for Cristiano Ronaldo to quickly equalize for Madrid in a high-octane game, which saw chances at both ends as well as several tough challenges.
Real should have had a late penalty when Alba cleared out Marcelo but referee Alejandro Jose Hernandez Hernandez somehow decided the challenge was clean.
The 33-year-old has won nine La Liga titles during his career-long association with Barca, also claiming six Copa del Rey crowns and four Champions Leagues.
The Catalan giants were crowned champions for the 25th time last weekend, and they already received a guard of honour before the encounter against Deportivo la Coruna.
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"We will look tomorrow [Monday] and see what damage has been done", Zidane said after the game on Sunday, as quoted on goal.com".
"Technology is going to be good for football, but it will take time to adjust, the important thing is that the games have rhythm, at the beginning it will be complicated, but there are plays that require it".
"They are games to enjoy, this is a different game, there's nothing like it".
Suarez admitted after the game: 'I think it was a small foul.
"Luckily we don't have VAR yet, or we'd still be playing", joked Valverde in his post-match news conference.
MF Ivan Rakitic, 8 - The Croatian was Barca's hardest worker and most useful player in midfield, distributing the ball well and battling hard.
Both sides pushed for a victor and Real could have had a penalty when Jordi Alba caught Marcelo but Barca clung on to remain unbeaten in the league with three games to go.
Relegated Las Palmas gave Getafe's slim European hopes a huge hit with a shock 3-0 win.