The Emirates, who salvaged a 1-1 draw in their curtain-raiser against Bahrain after a controversial late penalty last weekend, went top of Group A on four points from two games despite a hairy start in Abu Dhabi.
India captain Sunil Chhetri overtook Lionel Messi in international goals as the Blue Tigers stunned Thailand 4-1 in their opening game to earn comparisons with Indian cricket captain Virat Kohli for his heroics back home.
The veteran striker and Ashique Kuruniyan both forced smart saves from UAE goalkeeper Khalid Eisa before the home side drew first blood against the run of play.
Mubarak whipped the ball home from an acute angle four minutes before halftime for the Emirates, who were runners-up the last time the country hosted the Asian Cup in 1996.
Mabkhout sealed the points with a cool finish two minutes from the end -- his 47th goal in 75 internationals -- to give the scoreline a somewhat flattering complexion.
Until Mubarak's strike -- his first for his country -- the 2015 semi-finalists had been largely restricted to speculative pot shots that threatened little but the fleets of luxury cars in the stadium parking lot.
India pushed for the equaliser in the second half, Udanta Singh slamming a shot against the bar 10 minutes after the restart.
But India, who finished runners-up on their Asian Cup debut in 1964 when it was a four-team competition won by Israel, will still fancy their chances of reaching the knockout phase for the first time.
Thailand, sacked Serbian coach Milovan Rajevac after their humiliating loss to India, bounced back by beating Bahrain 1-0 in Dubai earlier on Thursday.