[6] Renger van der Zande rounded out the top six, in a crash-filled session with four drivers – Daniel Abt, Felix Rosenqvist, Rio Haryanto and Kimiya Sato – hitting the wall, with William Buller and Michael Ho also having excursions down escape roads.
Mortara only secured the top spot, after a late crash by Carlin's Jazeman Jaafar at Fishermen's Bend, which stopped the other drivers from improving their times.
Van der Zande finished the session in sixth place ahead of rookies Felipe Nasr and James Calado with Alexandre Imperatori and Abt rounding out the top ten.
Japanese trio Yuhi Sekiguchi, Hideki Yamauchi and Yuji Kunimoto were next up ahead of Formula 3 Euro Series runners Alexander Sims and Merhi.
[8] Jaafar ended the session in 20th after his late incident, ahead of Haryanto, Lucas Foresti, Hywel Lloyd, Sato, Rosenqvist, Rafael Suzuki, Adderly Fong, Daniel Juncadella – who also crashed at Fishermen's – and Ho.
[9] Muñoz was also among eight drivers to receive a five-place grid penalty for the qualification race by ignoring yellow flags, as well as Calado, Sekiguchi, Buller, Foresti, Webb, Yamauchi and Huertas.
When second qualifying finally did take place, Mortara set the pace again before the first of two red flags for Fong hitting the wall at the Solitude Esses.
[13] Mortara's teammate Vanthoor then usurped his time before the second red flag for Kunimoto hitting the wall, again at Solitude.
[13] Signature had a 1-2-3-4 clean sweep until the last lap of the session when Bottas found a clear run to vault his way back into second.
After Huertas' penalty, Rosenqvist, van der Zande, Juncadella, Vergne and Félix da Costa all moved up on the grid.
The rest of the grid lined up as Jaafar, Lloyd, Nasr, Imperatori, Suzuki, Calado, Webb, Sims and Muñoz (after penalties), Haryanto, Foresti, Kunimoto, Sato, Ho, Sekiguchi, Buller, Yamauchi and Fong.
Behind the leaders, Nasr ran wide and almost hit the wall on the outside of the bend but Calado lost rear grip on his car and spun into the barriers.
[16] Bottas' teammate Merhi soon caught up to the pack and moved ahead of the Zandvoort Masters winner and into fourth place.
Bottas finished fourth ahead of Wittmann, van der Zande, Vergne, Huertas, Félix da Costa and Juncadella.
[18] At the start, the Signature cars of Mortara, Vanthoor and Abt all made decent getaways while chaos ensued in the midfield.
Muñoz's crabbed Dallara also took out two further Räikkönen Robertson Racing cars as Sims, starting last after his crash at the Mandarin on Saturday, rammed into the back of Ho and both drivers were out as they could not separate themselves.
Mortara held the lead into Lisboa ahead of Abt, Vanthoor, Bottas, Wittmann and van der Zande.
Racing resumed with Mortara making a sluggish restart allowing both Abt and Vanthoor to attack for the lead down to Lisboa, running three-wide at one point.
[3] Ultimately, it was to be a short run out front for Abt, as later on the lap, he hit the barriers at the Solitude Esses and was lucky not to be collected by Vanthoor,[20] or any other drivers as his car skated along the wall on the tight, upper portion of the circuit.
[3] Mortara's pace picked up and he made short work of Vanthoor, taking the lead at Lisboa, and would not be headed again as he became the first driver to win consecutive Formula Three Macau Grands Prix.
Wittmann ran a lonely race to fourth ahead of van der Zande, who repassed Félix da Costa on lap eleven.
Vergne was seventh ahead of Merhi, who avoided the start-line shunt to move up from 22nd to eighth, with the top ten rounded out by Rosenqvist and Huertas.