After winning 77-75 at the buzzer in the first meeting between the sides back on November 25, Estonians Kalev threatened to pull off another escape when cutting a seven-point deficit to 59-57 in the final minute.
They fouled Roller and the experienced Germany national team point guard drilled both shots from the stripe for the four-point win.
Deutsche Bank improved to 2-2 with the victory while Kalev fell to 1-3.
The charity stripe is where Kalev Cramo lost the game because not only did Roller make his free throws at the end, but the Estonians were just nine of 22 (40.9%).
Nate Fox only made one of seven (14.2%) for the visitors.
The Germans moved in front for good in the second quarter.
With the game knotted at 16-16, baskets by Keith Simmons and Ilian Evtimov gave them a four-point advantage.
Lorenzo Gordon, who had game highs in points (18) and rebounds (11) for Skyliners, made a lay-up in the final minute of the first half to stake the team to a 33-23 lead at the break.
Kalev Cramo managed to stay within striking distance the entire second half but didn't threaten to come all the way back until the end.
Trailing 57-49, jumpers by Josh Pace and Kristjan Kangur reduced the deficit to just four before Fox twice went to the free throw line and made only one of two.
Nenad Vucinic's team then forced Deutsche Bank into a 24-second shot-clock violation and the Tallinn club called a timeout to discuss the strategy.
When play resumed, though, Pace was called for travelling and Kalev Cramo ended up fouling Roller who made two free throws for a 59-55 lead with 18 seconds to go.
Kevin Lyde made it a two-point game again with a lay-up but the Estonians fouled Roller again and he sank the late free throws to ice the victory.
Deutsche Bank overcame a poor night shooting the ball.
They were just four of 18 (22.2%) from long range and 13 of 21 (61.9%) at the free throw line.
Murat Didan's side was also 18 of 39 (46.1%) inside the arc.
They dominated the boards, out-rebounding Kalev Cramo 43-22.
Pascal Roller, player Deutsche Bank Skyliners:
"This was an important win for us. The game was not pretty all the time, because Kalev is a tough opponent and we had our problems on offense today. But I am happy that the spectators supported us and that we were able to give them back a win."
Murat Didin, coach Deutsche Bank Skyliners:
"Intensity and defense - this is very important in today's basketball. We showed this in our game today. I congratulate my players for their effort and energy. Now we are second in the group. We know it will be very tough to advance, but we have our chances and we believe in them."
Kevin Lyde, player BC Kalev:
"We started the game really good, but then we got soft. I should have given the team more on both ends of the floor. In the second half we picked it up, but Frankfurt hit big shots."
Nenad Vucinic, coach BC Kalev:
"Thanks to Deutsche Bank Skyliners for their great hospitality. They played better basketball today. After a good start we could not capitalize on our advantages. We played too soft in the second quarter and let them dominate us inside. Offensively we could not control the ball in the end and rushed the plays too much."