Estonia had won the first encounter between the sides 69-65 back on August 5 in Tallinn.
Playing at home this time, the Czech Republic broke open a close game at the end of the first half.
Leading 28-27 with 4:11 remaining in the second quarter, Benda hit a jump shot to take his points haul to 30-27 and spark a 13-0 Czech run to finish the quarter.
At the start of the second half, Jan Vesely dunked and Sokolovsky drilled back-to-back three-balls as the Czechs extended the run to 21 points for a 49-27 stranglehold on the contest.
They enjoyed a double-digit lead the rest of the way.
Estonia were 13 of 37 inside the arc compared to 21 of 43 for the Czechs.
The Baltic side made just two of 18 shots from long range while the Czechs were seven of 12.
The top two sides in the Relegation Round will stay in Division A.
Ukraine also beat Hungary on Friday to leave both sides with 2-2 records.
Czech Republic Head Coach Michal Ježdík:
We have played good game in defence. That means that we made pressure and we had a lot of free shots. Both our older players Ladislav Sokolovský and Petr Benda played a great game and they were the key to win this game. These three matches were very demanding, but we had one big advantage - we needn´t to travel and we could focus only on our performance.
Czech Republic Player Ladislav Sokolovský:
I think that the difference of 26 points is very nice, but it was not so easy as it looks like. I agree with our coach, we were aggressive and we made some easy baskets. That was one key to win the game. The second key were our great fans and I would like to thank them all for their support. They were our sixth player on the court.
Estonia Head Coach Ullar Karde:
It was third game on the road and we had a mental problem, because it was our sixth game in eighteen days for us, so we spent the most of time in bus or hotel. I congratulate to opponent, but I still feel bad, because we didn't fight tonight.
Estonia Player Tanel Sokk:
When we started we wanted to try too much to make the game with three point shots, but it was difficult to win with these stupid player´s mistakes. We were nervous from the beginning and that was also the reason of our lost.