Smalling caught the Barcelona star in the face with his arm as the two challenged for an aerial ball in the first leg of their Champions League quarter-final.
Messi was unusually quiet but still managed to have the last laugh as he played a key role in the only goal of the game that saw Luke Shaw turn past into his own net.
It was a feisty affair between two European heavyweights and Smalling was involved in incidents with both Messi and his Barca team-mate Luis Suarez.
However, he insists there is no problem between the players and revealed they discussed it after the game.
“Yeah, we spoke after,” Smalling said. “I didn’t realise at the time actually that I caught him like that.
“But, after the game we just had a brief chat, shook and hands and he said ‘yeah, it was an accident’.
“[I spoke to] Suarez after as well. We had a good tussle and he just shook my hand after and we said good luck.
“It’s nice when you can have that battle on the pitch and then there’s full respect after game.
“Ultimately you’re just trying to do your best and enjoy the game.”
The two sides face each other today, Tuesday 16th April 2019 in Spain at the as big underdogs as they need to score at least once at the Nou Camp.
However, manager Ole Gunnar Solskjaer believes there were positives to take from a game in which United were not overawed by one of the favourites to win the competition outright.
"There were pluses and negatives,” the Norwegian said.
“We started sloppy and a bit nervous. After their goal we settled and played well.
"We had very good individual performances in midfield. At times it felt like a proper United team - the crowd were behind us, we got out wide and got crosses in.
"We didn't start great, but it was a great goal and movement from Messi and Suarez but they're fortunate it comes off Luke Shaw.
“It's a blow but we settled well. We're still in this tie."
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