Pescara hosted Lega Pro A side Renate and although youngster Gianluca Caprari gave the home team an excellent start with his third-minute opener, the away side fought back to force penalties.
Damien Florian's equaliser just after half-time was enough to secure extra-time and, after the two sides could not be separated, Pescara eventually triumphed 6-5 in the shoot-out.
Latina and Novara also drew 1-1 after extra-time but the latter advanced to the third round as they emerged 4-3 victors following spot-kicks.
There were also shoot-out triumphs for Casertana (4-3) and Como (3-1) after they both drew 0-0 at Crotone and Frosinone, respectively.
Arguably the best match of the day saw Livorno surprisingly dumped out by visitors Bassano Virtus, losing 4-2 at home to the third-tier side.
Andrey Galabinov initially opened the scoring for the hosts but Bassano led with 10 minutes remaining in the first half when Simone Iocolano scored from the spot, following Tommy Maistrello's equaliser.
Marco Moscati then equalised in the 41st minute but a quick-fire double from the away side in the final three minutes earned Bassano a memorable win.
Giusto Priola struck in the 87th minute before Filippo Stevanin secured victory for the fourth-tier side in stoppage time.
There was also late drama as Brescia beat Pro Vercelli 2-1.
Serie A stalwart Andrea Caracciolo netted twice for the home side, with his second coming in the 90th minute to secure a slender victory, while Pisa also left it late when defeating Carpi 2-1.
Bologna slumped to a disappointing home defeat as they were beaten 2-1 after extra-time by L'Aquila, with Claudio de Sousa getting the decisive goal in the 103rd minute.
Varese and Juve Stabia fans were treated to a five-goal thriller at Stadio Franco Ossola but the majority of those in attendance will have left content after the hosts won 3-2.
A Felipe Avengatti double was enough for Ternana against Catanzaro as they won 2-1, while Cremonense and Bari 1908 defeated Trapani and Savona, respectively, by the same scoreline.
FeralpiSalo looked to be heading for extra-time at Perugia but their hosts netted twice in the final 12 minutes to earn a spot in the next round, while Catania join them after squeezing past Sudtirol 1-0.
Avellino also booked their passage with a 2-0 success over Venezia but Alessandria's Coppa campaign ended in a 1-0 loss at Virtus Lanciano.