United dominated possession but struggled to break down CSKA until their skipper struck to draw himself level with Denis Law as the club's second-highest scorer on 237 goals.
His header from Jesse Lingard's cross was United's first goal in 404 minutes - a run that included goalless draws against Manchester City, Middlesbrough and Crystal Palace.
Prior to the goal, the Old Trafford crowd were clearly unhappy when Martial was replaced with Marouane Fellaini after 65 minutes.
News that makes sense
Your trusted source for staying up-to-date with the world around you. Get free daily news updates and analysis, straight to your inbox.
"I'm not deaf. That's the opinion of the fans but afterwards they shall not be disappointed," said Van Gaal.
"I'm very happy because I put Rooney again in the striker's position and he scored."
Rooney's strike sent United to the top of their group and midfielder Bastian Schweinsteiger underlined the importance of the goal.
"It was a big moment for us because we hadn't scored a goal in the last few matches so it was very important," Schweinsteiger was quoted as saying by the club's website (www.manutd.com).
"For us it was very important to win at home. Also, in the group, we are now at the top and we have to win the next match against Eindhoven, but the situation is much better now," the German international added.
United need just one win from their last two group matches, at home to PSV Eindhoven and away at VfL Wolfsburg, to reach the last 16.
Schweinsteiger said he hoped the floodgates would now open for Rooney, starting with their Premier League game against West Bromwich Albion on Saturday.
"I am also happy for Wayne that he scored his goal and I think it will give him a lot of confidence and I hope he can use this confidence in the next match."
(Reporting by Simon Jennings in Bengaluru)
