The 23-year-old has been in stunning form in 2019-20 thus far, scoring 18 goals in 17 Bundesliga matches to help Leipzig maintain a two-point advantage atop the league standings heading into the second half of the season.
Werner was reportedly close to joining Bayern before the season, but the Bavarians did not make a formal bid.
Salihamidzic has now helped to shed light on that decision, suggesting that the striker is not a good fit for their system and that pairing him with star forward Robert Lewandowski would be a tall order.
"Timo Werner is a good player who played an excellent first half of the season," Salihamidzic told Bild.
"However, we have Robert Lewandowski. Robert is a striker who fits our style of play perfectly.
"Robert has the ability to orientate himself in a tight space, the technical ability to move in tight spaces and to find extraordinary solutions with the ball.
"With his speed, Timo Werner needs more room, which he had in the system that Leipzig played. The system at RB has now changed, but it is still not as tight at the front as it is with us."
Those sides will have to wait until the summer to move for Werner, however, with the striker keen to chase a Bundesliga title with Leipzig and a European crown with Germany at Euro 2020 before addressing his future.
Chelsea are keen on a summer move for Werner as well as Borussia Dortmund star Jadon Sancho, with the club expected to spend big after they were banned from signing new players last summer.
Werner and RB Leipzig will return from the winter break with a Bundesliga match against Union Berlin on Saturday.