Southgate's men lost 3-2 in Tuesday's international friendly at the Stade de France, despite the Real Madrid centre-back seeing red for bringing down Dele Alli for a penalty that was converted by Harry Kane early in the second half.
France supporters were fuming when, after a one-minute delay, referee Davide Massa opted to send off Varane, having consulted his two video assistants.
Southgate felt the decision was most likely accurate, but warned the VAR system, which is being trialled ahead of potential use at next year's World Cup, will not produce 100 per cent accuracy.
"I have not seen it again, but from my initial view I thought it was the right call," Southgate told reporters.
"It looked from where we were a clear penalty and therefore a sending-off, but if people say otherwise I would need to see it again.
"I assume the referee wanted to make sure and if he has got that technology to do that, then it is a sensible decision.
"But clearly even with video not every decision will be 100 per cent — you won't get every single decision right. There will still be an element of one person's judgement within that."
Kane's penalty levelled the match at 2-2, but, despite being a man down, France rallied to victory thanks to Ousmane Dembele's winner.