Messi put the Eredivisie champions to the sword in the reverse fixture at the Camp Nou in September when he bagged a hat-trick in a comprehensive 4-0 win.
However, the Argentine star will miss Tuesday's Group H clash in Amsterdam with a hamstring injury - a factor De Boer believes works in his side's favour as they battle with Milan and Celtic to finish second in the pool behind Barca.
Nevertheless, with the likes of Neymar, Pedro and Alexis Sanchez at Barca coach Gerardo Martino's disposal, the Dutchman warned Ajax to still be wary of the Spanish champions' attacking prowess.
"Our goal is to finish second in the group so for us it's better when they play without Messi," De Boer said.
"On the other hand, they've lost few points in the league and in this competition without Messi. Of course it's a big loss for Barcelona because Messi is responsible for a lot of goals and assists, so they will miss him.
"But I think they're team is still reasonably good."
De Boer went on to insist Ajax will look to control the game, regardless of the quality of the opposition.
"We always try to dominate, inside and outside the Amsterdam Arena - we'll try to do it now as well. At Camp Nou, we played some pretty good at some moments during the first half, we have to remember that.
"In the second half we found out that we shouldn't give so much space away."
The 43-year-old also confirmed striker Danny Hoesen and midfielders Davy Klaassen and Lerin Duarte should be available for the game, but Lasse Schone is still a doubt.
