Baker allegedly lifted halfback Nick Stirzaker from the ground in the 12th minute and dropped the Rebels player while his feet were in the air.
On review of the match footage, the citing commissioner deemed the incident had met the red card threshold for foul play, leaving Baker to face a hearing next week in front of the Sanzar judicial officer.
Aside from Baker's indiscretion, the Highlanders will be happy with four points from a game in which they were short of their best.
The victory is the southern side's third of the competition, matching their win total from 2013, while it moved them to within a point of the Blues for second spot in the New Zealand conference.
The Highlanders will host the Bulls next week and Jamie Joseph's team will be eyeing the opportunity to further establish themselves in the playoff picture.
Joseph's counterpart, Tony McGahan, wasn't left quite as impressed after Friday's encounter, with his Melbourne side letting slip another golden opportunity to crack their first overseas Super Rugby victory.
For the third time in as many games in New Zealand, the Rebels lost by four points or fewer, matching the home side in scoring three tries but earning only a bonus point for their efforts.
"The players are really frustrated that they left a result out on the field," McGahan said. "They felt they were in good control of the ball and they defended for good periods."
- Herald on Sunday