The German topped the morning session from the midway point before improving on his personal best at the very end, eventually posting a 1m05.301s which left him more than two tenths clear of Nick Cassidy.
A red flag was deployed shortly after the opening five minutes when Oliver Rowland went off at Turn 1, the Mahindra driver making light contact with the barrier but unable to get underway again due to a technical issue.
Once the session resumed after more than a five-minute delay Sebastien Buemi moved to the top of the times with a 1m06.311s, the Envision Racing driver one-tenth faster than Jake Dennis.
The Andretti Autosport driver went ahead of Buemi with his next effort – a 1m06.109s – but was dropped back to second moments later as Buemi responded with a 1m05.686s.
It left him more than two tenths clear of Jean-Eric Vergne, as the DS Penske driver moved into second with the Jaguar machines of Sam Bird and Mitch Evans occupying third and fourth.
A time of 1m05.600s by Vergne sent him to the top of the times shortly before the halfway point of the session, which was extended by seven minutes following the red flag delay to retrieve Rowland’s stranded car.
Gunther’s 1m05.444s was good enough to put him fastest with 15 minutes remaining as Stoffel Vandoorne moved into third, less than two tenths off the Maserati MSG driver’s best.
The top of the order remained unchanged until the final minutes as Antonio Felix Da Costa moved into third, splitting the DS Penske drivers with a 1m05.616s, but at the chequered flag Cassidy moved into second with a 1m05.556s, to jump ahead of Vergne, da Costa and Vandoorne.
Despite being fastest Gunther lowered his time further with his last effort to move 0.255s clear at the top of the times.
Vandoorne had earlier topped FP1 on Friday evening, posting a 1m05.803s on his final lap to put himself +0.085s ahead of Dennis.
The Andretti Autosport driver had occupied the top spot for the final third of the 30-minute session with a 1m05.888s before being shuffled back to second by Vandoorne’s late effort.
Maserati MSG enjoyed a strong session, Gunther finishing third and Mortara fifth – the latter having his front wing replaced after damaging it against the barrier on the exit of Turn 4 early in the session.
Vergne was sandwiched between the pair in fourth, less than two tenths behind his DS Penske team-mate at the top of the times, as the Jaguars of Bird and Evans completed the top seven.
Da Costa occupied eighth while Porsche team-mate and championship leader Wehrlein was down in 17th, seven tenths off the pace.
