Du Plessis has signed a two year deal with Montpellier and Van der Merwe will join Clermont, also after the completion of the Absa Currie Cup competition.
The BBC's High Performance Manager, Xander Janse van Rensburg said talks with both players have been ongoing for some time.
"We want to thank both players, who were upfront with us from the start about offers from abroad. Flip has been a loyal servant to the Vodacom Bulls since 2009 and always made it clear that he would consider offers from abroad after the 2015 Rugby World Cup, especially as he does not have a Springbok contract. He has been a tremendous asset to the whole team and franchise over many years," Janse van Rensburg said.
"Jacques is one of the real upcoming stars in the game and this offer received from France is testament to that. We have been negotiating since June 2014 and he has indicated that he would like to return to the Bulls after the two years. That is good news to us, as he should also be in Springbok contention by that time."
The Vodacom Bulls have some good back-up coming through the ranks, as they have planned for a possible loss of players after the RWC 2015.
"We have planned for events like this and have some of the best young locks in the country on our books already. Guys like RG Snyman, Dennis Visser, Nicolaas Janse van Rensburg, Marvin Orie, Irne Herbst and Jason Jenkins are all amongst the best in their age groups and will be able to compete at a very high level," Janse van Rensburg said.
"It remains a massive battle to compete against the massive offers from abroad, especially as the exchange rate counts heavily against us, but we are confident that through good planning and scouting, we will be able to remain a very competitive franchise at all levels."
The BBC also confirmed the release of Ulrich Beyers, who will join Bordeaux-Begles in France with immediate effect.