Alli was impressive in England's opening group game, a 2-1 win over Tunisia, until he picked up a thigh injury which kept him out of the 6-1 crushing of Panama and 1-0 loss to Belgium.
Ruben Loftus-Cheek deputised for the Tottenham Hotspur man in those games but, while Southgate has yet to name his team, it is likely Alli will return alongside Jesse Lingard and Raheem Sterling as part of a trident supporting striker Harry Kane.
"For any player to miss matches at this level when you have worked so hard to get to this stage is very difficult," Southgate said when asked about Alli's absence.
"We didn’t see any point in bringing him back too early – he is absolutely fine now," said the England manager who believes Alli has the ability to penetrate the Colombia defence.
"What does he bring? The timing of his runs, that ability to see spaces in opposition defences, time his runs into the box and finish.
"That hasn't always happened for us as much as for (his) club up to this point but there is no doubt he has the ability and the techniques to do that.
"I thought his performance against Tunisia was really top, the way he pressed, his work without the ball was outstanding," Southgate added.
That is an aspect of the game that the England manager's tactics requires given his use of three forward-looking midfielders.
"We are a team where we don't carry any passengers, everybody has to really press and work for the team, and if our midfield players, our creative midfield players, are doing that as well then that is a really good sign," said Southgate.
He repeated the mantra that his team were not looking at the possible fixtures beyond Colombia but said they were aware they had a historic opportunity.
"It is over 10 years (2006) since we won a knockout fixture so for this team this is a brilliant opportunity to go beyond where more experienced teams have gone before.
"I think they are relishing that chance, the energy in training today was really good... we are viewing the game as one against an opponent we really respect.
"These are the games you want to be involved in, the games that matter, the lads have the chance to write their own stories now," he said.
(Reporting by Simon Evans; Editing by Ken Ferris)
