Ewan edged Irish rider Sam Bennett as both riders pushed in the final sprint to the top of Hatta Dam east of Dubai.
The win was the Lotto-Scoudal rider's second consecutive win in this stage after claiming line honours in 2019.
After two stages, the Aussie rider holds a 12 second lead in general classication and will where the red jersey in Tuesday's stage 3.
The second stage was a tough day for returning British star Chris Froome who was dropped from the peloton with 8km to go.
Stage one winner Pascal Ackerman also struggled to keep pace, The German Bora-Hansgrohe rider also fell away in the latter stages.
Stage three will be a 184km section from Al Quadra Cycle Track on the outskirts of Dubai before finishing with a mountain climb up Jebel Hafeet.