The duo are competing for one spot to play in Chelsea's midfield, next to N'Golo Kante.
Matic was a regular for most of the campaign, but Fabregas has featured a lot more over the last few months.
The latter has made the most of his opportunity, with statistics supplied by EA Sports showing that he has the best minutes per assist record of anyone in the Premier League who has played over 180 minutes this term.
The Spain midfielder (seven assists) has created a goal every 104 minutes, while Matic's (six assists) have come every 333.
But Conte said it's still hard to choose between them as he prepares to face Stoke at the Britannia Stadium tomorrow.
He explained: “Now I have all my players top of their form, for sure it's not easy for me to make the best decisions.
"In this case (Fabregas v Matic) it's important to manage the situation and see game by game.
"If, for example, we have to face a physical team who are very strong in set-plays, you must consider a lot of situations before making the right choice.
"For sure, Cesc gives you great quality, great fantasy and assists. Yeah, but it's important for me, above all at this point of the season, to manage very well the situation and understand when it's right, for example, to play with Cesc or with Matic.
"We are talking about two great players, for sure with different characteristics. Nemanja is more physical, more technical, less fantasy than Cesc. Cesc has more fantasy but is less physical than Nemanja.”
Of the 27 League games Chelsea have played, Fabregas has been named in the first XI just seven times.
However, Conte has learned to appreciate the former Arsenal and Barcelona star even more because of the way he's handled the situation.
He added: “Cesc is showing he has a great impact for us. I hope to finish the season in the right way and to try to win (trophies). But for sure Cesc has shown himself to be a great professional but, above all, a great player.
"I'm very pleased to see that in him, his commitment and work-rate. This season he faced a new situation.
"In the past, Cesc has always played every single game. It's not easy to change. But, for sure, Cesc showed me that he is not only a great player but a great person.
"I think, this season, he has improved a lot in all aspects and, for me, he is a really, really important player.”