Winks earned his first England cap as Harry Kane’s first-half penalty secured a 1-0 win in Lithuania.
And Southgate was pleased with the way his side managed to grind out a result despite his experimentation with the line-up.
“We haven't scored the number of goals we would have liked to but we gave three full debuts and wanted to try something,” he said.
“A bit more quality in the final third is what was missing.
"They had a packed defence, we were a fraction off. Running at people on that surface doesn't work, we needed one-twos and quick passes.
"It's a completely different challenge against Brazil and Germany next month.
"Put today into context. We made seven changes, that inevitably means that you will be disjointed at times. Harry Winks showed real calm, his use of the ball was excellent.
"Three at the back worked in some aspects but we are still open in counter-attack."
Winks was called up to the squad after Manchester City midfielder Fabian Delph was forced to withdraw through injury.
The occasion didn’t faze the Spurs midfielder as he looked comfortable in possession and was unlucky not to cap his debut with a goal.
He said: “It’s been a dream week for me. To be called up into the seniors is fantastic.
“I nearly scored. The keeper made a great save off my left foot, if that had gone in it would have been brilliant.
“I was quite surprised when I got the call to step in, but obviously I’m happy to step in. It was brilliant for me.”
Victory means England remain unbeaten throughout qualification and finish top of Group F, six points clear of Slovakia.
