The five-time Ballon d'Or victor was left battered and bruised after a harsh challenge from Smalling just past the half-hour mark in United's first-leg quarter-final 1-0 loss to the Blaugrana on Wednesday. Juventus almost won it when Douglas Costa hit the post in the 85th.
"Once again Ronaldo proved to be on a different level", said Allegri. "His timing and movement is different to everyone else".
"Ajax have great qualities".
"We suffered after their goal because we were a bit shocked to concede immediately after the break but we defended well and finished the game better".
The deflected header turned out to be the only goal of the game and United are now faced with an uphill struggle to reach the semi-final stage with the daunting prospect of needing to score at least two goals at Camp Nou to advance.
Ajax had set up this tie by ending Real Madrid's European hegemony in the previous round after a thrilling 4-1 victory in Spain, and maintain hope going into the return.More news: Top Obama WH Lawyer Charged With Lying About Foreign Collusion
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Once confirmed, this will be Allegri's fifth - but the ex-AC Milan manager said he wants the players to remain focused on the clash with Ajax even if the title is secured away to SPAL.
Starting XI: Onana (6); Veltman (6), De Ligt (7), Blind (7), Tagliafico (7); Schone (6), De Jong (8*); Ziyech (8), Van De Beek (7), Neres (8); Tadic (7).
In actual fact, United will be kicking themselves because they went up against as poor a Barcelona display as they are likely to see for a while, and still came out on the losing side.
The latter was kept largely quiet, but he was afforded too much time and space by the Ajax defence as he opened the scoring with the last act of the first half.
Ronaldo headed home Joao Cancelo's cross on the stroke of half time to add to his tally as the competition's all-time top goalscorer.
Juventus appeared to of read the blueprint of a ideal Champions League away performance prior to kick-off, as despite being second best for large spells in the first-half, they converted their big chance when it fell to them. However, despite exerted pressure after that, Ajax could not get a victor, and Costa almost delivered a late sucker punch when he struck the woodwork.