Pavard played a key role in France's World Cup win at Russia 2018 and reports of a move to Bayern have persisted since, although both parties have previously denied any agreement.
Salihamidzic has now confirmed that terms have been agreed for a switch come the end of the season, with Pavard to sign a deal that will keep him at Bayern until 2024.
"I can confirm that Benjamin Pavard will join us on a five-year deal from July 1, 2019," he told reporters in Doha.
Pavard is contracted to Stuttgart for another two years, but Salihamidzic did not disclose details of a fee for the 22-year-old.
The defender, who can play at centre-back as well as right-back, moved to the Bundesliga from Lille in 2016 and soon established himself as a star man for Stuttgart, starting all 34 league games last season.
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He has also played 14 times in the Bundesliga this term, but Stuttgart are toiling in 16th place.
Pavard played in six of France's seven games at the World Cup finals, only missing their final group game against Denmark, and he scored his first international goal in the last-16 clash with Argentina.
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