Most of the squad play in La Liga where the system is not used and have therefore not had the experience of frequent pauses in play which are likely at the finals in Russia, where VAR will be rolled out for the first time at a World Cup.
"We need to prepare for it (VAR) because there will be moments that we are not used to, we have to be prepared for stoppages and restarts," Lopetegui said.
"We need to understand what the rules are, what the referee's priorities are so we can act accordingly. This is something new to us as it doesn't exist in Spain and we need to be ready for it at the World Cup where it will exist."
Spain have been drawn in Group B at the World Cup and face UEFA Euro 2016 winners Portugal in their first game in Sochi before playing Iran and Morocco.
"We'll be meeting the champions of Europe, the best team in Asia and the best team in Africa," Lopetegui added.
"It's a difficult group but every group is going to be tough. After all, this is the World Cup."
Spain had begun to stagnate under Vicente Del Bosque after winning their first World Cup in 2010 before their triumph at Euro 2012 but they have been on a resurgent run since Lopetegui became coach in July 2016.
They breezed through qualifying to top their group and are unbeaten in 18 games, while they outclassed Italy 3-0 in qualifying and hammered 2014 World Cup runners-up Argentina 6-1 in their last friendly outing in March.
"Our success has been the fruit of work over these two years but the people responsible for that are the players," Lopegegui said.
"The players have shown passion, determination and conviction for the way we want to play, everyone wants to be part of this team and we want to build on that sentiment.
"The first stone was cast by the players and we have tried to design how we want to play and what team we want to be and the players have shown a lot of determination to keep growing as a team."
Lopetegui knows the Spain set-up inside out due to many years spent with the country's youth teams, including winning the European Championship with the under-19s in 2012 and the under-21s in 2013.
He has worked with many of the players who will be in the 23-man squad he will take to Russia since they were teenagers, including Manchester United goalkeeper David de Gea, Atletico Madrid midfielders Koke and Saul Niguez and Real Madrid playmaker Isco.
He can also count on tournament veterans such as Andres Iniesta, Sergio Ramos, David Silva, Sergio Busquets and Gerard Pique, who were all part of Del Bosque's side.
"A lot of the players have been in the national team since they were children and that's important because since a young age they've been used to going to international tournaments, playing against the best players from every country," Lopegegui said.
"The best team is always the best mix of different generations, we have that and we'll try and make sure it's a good mix."