After failing to work a quicker delivery on the leg side, Warner - a lefty - turned into a right-handed batsman to face the next ball.
Warner became the second Australian to injure his elbow playing in the Bangladesh Premier League on Wednesday night as he hit 61 not out for his Sylhet Sixers, after Steve Smith was also hurt in the competition last week.
Warner was 47* mid-way through the 19th over when, after struggling to get Gayle away, he switched his stance and began batting right-handed.
Warner will return to Australia where he is likely to need six weeks to recover from the injury.
"David has reported some pain in his right elbow", a Cricket Australia spokesperson said.More news: Shopko Files for Bankruptcy Protect, Closing 38 More Stores
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The right-hander has played 184 T20 matches and scored 4,815 runs with four hundreds and 31 fifties.
"We will have a clearer understanding of extent of the injury once he has been assessed".
Australia captain Smith and Warner, his deputy, were both given 12-month suspensions from state and global fixtures by Cricket Australia for their roles in a ball-tampering scandal during a Test match in South Africa in March a year ago.
That over from Lamichhane gave Sixers a stranglehold in the game as Tanvir and Rana negotiated with the defence as Riders ultimately fell 27 runs short.
Both Smith and Warner's 12-month bans end on March 28 and the duo was expected to feature in Australia's last two matches of the five ODIs against Pakistan in the UAE.
Nonetheless, Warner-led Sixers are at the last spot on the seven-team table with just one win from four matches. He joins Steve Smith as the other Australian player to miss the tournament due to the same injury. He will play no part in the three-Test series that starts on January 23.