The 19-year-old conceded a first half penalty when the United striker handled inside David De Gea’s penalty area.
And CSKA striker Seydou Doumbia broke the deadlock after David De Gea had initially saved Roman Eremenko’s spot-kick.
But Martial made amends in the second half with a brilliant 65th-minute header to secure a point for the visitors in Moscow.
However, United captain Rooney, who missed a second-half chance in the Russian city, reflected on a disappointing stalemate with their Group B opponents.
Rooney wrote on his Instagram page: “Gutted not to come away with the win last night but still an important point in a tough game. Time to focus on the big game against City this weekend ”
The Red Devils are in second place in Group B and two points behind Bundesliga Wolfsburg ahead of their return game against CSKA at Old Trafford.
Rooney is still waiting for his first goal in the Champions League group stage after netting three times in the play-off win against Club Brugge.
Martial has scored five times in nine games in all competitions for the 20-time English champions after his £36m move from Ligue 1 outfit Monaco in the summer transfer window.
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