Pacos Ferreira were searching for their first win in Group E but found visiting goalkeeper Denys Boyko an immovable object for most of the frustrating encounter.
Dnipro kept energy in reserve, and late smash-and-grab goals from Ruslan Rotan and Yevhen Konoplyanka booked them the second group victory they needed to stay in touch with Fiorentina.
Antonio Filipe was the first goalkeeper to get a feel of the ball. He caught Rotan's sighter before repelling Konoplyanka's snapshot from 12 yards.
Bebe came close to opening the scoring at the other end in the 16th minute but his shot from Jean Seri's free-kick brought a solid parry from Boyko.
Nikola Kalinic emerged as Dnipro's biggest threat before the break and, after his weak shot sailed over the bar, he sent Filipe sprawling with a close-range effort in the 34th minute.
Sergio Oliveira checked Boyko was still paying attention after half-time with a drilled effort that the Dnipro keeper had to punch away.
He would not get close to Rui Miguel, however, as the attacking midfielder headed Manuel Jose's free-kick over the bar.
Boyko was given another wake-up call when Ruben Ribeiro stung his palms with a rasping drive in the 74th minute.
Nine minutes later, Dnipro took the lead against the run of play.
Rotan was the beneficiary as Konoplyanka pulled the ball back from a short-corner routine to leave Filipe rooted to the spot.
He would not move far in the 86th minute either as the Ukrainians plundered a quickfire second before their hosts could reorganise.
Provider turned goalscorer as Konoplyanka caught the Portuguese defence cold at the end of a swift counter-attack.
He burst past two men on the left wing before cutting inside and poking the ball home to rubber-stamp the three points.