Jamie Vardy's 26th-minute strike appeared to have the hosts on course for victory until Italy were awarded a spot-kick in the closing minutes of the friendly fixture.
England debutant James Tarkowski was adjudged to have fouled Federico Chiesa inside the area, albeit replays showed the defender appeared to accidentally stand on the substitute's foot.
Still, referee Deniz Aytekin pointed to the spot after reviewing the footage, allowing Lorenzo Insigne to draw Italy level in the 87th minute.
"I’m glad it’s not a World Cup!" Southgate told ITV Sport.
"I think the ruling is clear and obvious [errors] and I don't think that was clear and obvious. It's one you can debate forever.
"It looks like Tarkowski stands on him, but that’s in the motion of running and it looks like he was on his way down anyway.
"It's designed to stop the deliberate handball or something like that. I think the referee had a good view.
"I don't think with incidents like that it [VAR] is going to clear things up 100 per cent. An obvious handball or offside, things like that, but anyway we have to get on with it."
3 - England have drawn three consecutive matches at Wembley, or indeed three consecutive home matches, for the first time in their entire history. Stalemate.— OptaJoe (@OptaJoe) March 27, 2018
Despite conceding for the first time in six games, Southgate still saw plenty of positives in England's performance.
The game offered those in the squad a final chance to impress their manager before he names his provisional squad for the World Cup.
"The first five minutes we were very sloppy. After that we settled into the game and probably created more chances than we have done in a lot of matches," Southgate added.