The prize was established to recognize the contribution of family-owned firms to both the economy and their local communities.
Previous winners have included Lego, Ayala Corporation and Hermès.
To be considered for the award, businesses must be at least three generations old.
The Lieshout-based brewery is one of the oldest privately run companies in Holland.
Founded by 1680, it has been owned and run by seven successive generations of the Swinkels family since 1764.
Some 28 family members currently work in the business.
Bavaria turned over £361.9 million in 2014 and sold 5.6 million hectolitres of beer. It is the second largest brewery in The Netherlands after Heineken.
It exports to over 120 countries worldwide and employs over 1,000 people across its global operation.
Jan Renier Swinkels, chief executive: “The task of each generation is to find out what's happening in society and adapt to it. It is a matter of staying ‘fresh’.
“It is fantastic that we are presented with the IMD-Lombard Odier Global Family Business Award as a family. Fantastic recognition for the passion and craftsmanship with which we have been brewing beer and running our brewery for more than 300 years now.
“As a family, you always look at the long term. Every generation has the brewery on loan from his children and grandchildren. That means continuity takes priority over everything.
“This beautiful award is therefore not a start or end point. It is a token of recognition and another incentive to continue to follow our dream: to hand over the brewery in an even better condition than it already is.
“During all those years, we have achieved a lot thanks to our joint adaptability. The world is always changing and if you want to grow, you have to cater for that.
"We want to thank everything, our members of staff in particular, who contributed to our beautiful brewery at it is today.”