Top seed Isner prevailed in a rain-delayed yet ultimately entertaining contest under the lights at Atlantic Station to set up a crowd-pleasing semi-final clash with Andy Roddick.
Roddick, seeded fourth in Atlanta, beat another American Michael Russell 6-3 6-4 to book his place in the final four.
Roddick and Isner know each other well and will feature on the same US team at the upcoming Olympic Games in London.
Roddick holds a slight edge in their head-to-head record: the 29-year-old leads Isner, 27, 3-2.
In the day's other semi-final, eighth seed Go Soeda sprang something of an upset in the all-Japanese clash with Kei Nishikori.
Soeda downed his third-seeded compatriot 6-2 6-1 and he will now play Gilles Muller of Luxembourg, who beat Australia's Matthew Ebden 6-4 6-4, for a place in the final.
In Gstaad, Bulgarian starlet Grigor Dimitrov beat Lukasz Kubot 6-3 6-2 to move into the semi-finals.
Dimitrov, 21, made relatively light work of the 30-year-old Pole, who had surprised defending champion and second seed Marcel Granollers in the previous round.
The world number 61, who is his country’s top-ranked player, will face Brazilian Thomaz Bellucci in the last four after he beat fifth-seeded Spaniard Feliciano Lopez 6-3 6-3.
Janko Tipsarevic, the number one seed in Switzerland, wasted no time in advancing into the last four with a 6-2 6-1 win over qualifier Jan Hernych.
After 62 mintues, the Serbian set up a showdown with France's Paul-Henri Mathieu, who needed three sets to overcome Ernests Gulbis 4-6 6-1 6-4.
In Hamburg, Tommy Haas ran out victorious against fellow German Florian Mayer, winning 6-1 6-4 as form trumped the seedings. Mayer was seeded seventh, but Haas recently won the Halle tournament, beating Roger Federer in the final.
Haas faces Marin Cilic next, after the Croat shaded Albert Ramos 6-4 7-6 in two close sets.
On the other half of the quarter-final draw third seed Juan Monaco of Argentina beat Frenchman Jeremy Chardy 6-3 7-5.
Monaco will play top seed Nicolas Almagro, who ousted in-form sixth seed Phillipp Kohlschreiber 7-5 7-5 in a match where neither man were able to get their serve going.