The central defender, who is on loan from Swansea City, headed home in the 87th minute to give Garry Monk his first league win at Elland Road.
Whites substitute Chris Wood had given the home side the lead in the 65th minute before Bartley's Swansea colleague Marvin Emnes, who is on loan at Blackburn, thumped home a 77th-minute leveller from 20 yards.
But Bartley came up with a header from Alex Mowatt's free-kick to send Leeds up to 17th on the Championship table with Owen Coyle's Rovers remained rooted to bottom spot.
Other loanees in action in West Yorkshire were Torino defender Pontus Jansson for Leeds along with Al-Arabi's Pablo Hernandez and Sporting Lisbon's Hadi Sacko, while Southampton striker Sam Gallagher, fresh off a goal against QPR on the weekend, went for a full 90 for Blackburn and Watford's Tommie Hoban also played the full game in defence.
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