Milwaukee improved to 7-4 since acquiring Ellis from Golden State and moved within a game of New York for the final post-season spot in the Eastern Conference.
Charlotte came back from a 10-point deficit in the third quarter to take a one-point lead with 3:44 to play but two free throws from Ellis put Milwaukee back in front for good and touched off the late surge.
Byron Mullens scored a career-best 31 points for the Bobcats, who have lost 10 straight and have won only seven times in 52 games this year.
Veteran Charlotte forward Eduardo Najera was struck in the head during the second quarter and was taken to a hospital with what a team spokesman said was a fractured frontal lobe.
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