In a rollercoaster game, Schalke squandered a two-goal lead after coming from a goal down as Adrien Silva struck twice in the second half for 10-man Sporting, who had Mauricio sent off after half an hour, to draw level.
But Cameroon international Choupo-Moting, who had come on in the second half, kept his cool to win the game for Schalke deep in stoppage time with a penalty awarded for handball, with the Portuguese protesting at the decision of Russian referee Sergei Karasev.
TV replays showed the ball hit Jonathan Silva's head rather than his arm.
It is now two wins from two games in all competitions for Italian Di Matteo, who won the Champions League as Chelsea's caretaker manager in 2012.
"Today we were very lucky," Schalke forward Huntelaar said. "In the second half we were much better than in the first one, we were leading 3-1 with 11 players against 10, but then we gave it away. Normally you don’t win matches like this."
Portugal winger Nani, on loan from Manchester United this season, had put the visitors ahead on 14 minutes before Schalke levelled through Nigerian Chinedu Obasi with the Portuguese down to 10 men after the dismissal of Mauricio in the 33rd.
Schalke are second in Group G on five points, two behind leaders Chelsea, who crushed Slovenia's Maribor 6-0. Sporting are on one.
Sporting coach Marco Silva named an unchanged line-up to the one that beat Porto 3-1 in the Portuguese Cup on Saturday and they got off to a good start with Algerian Islam Slimani going close early on.
With the roof closed over the Auf Schalke Arena on a rainy Ruhr valley evening, Nani opened the scoring when he was left completely unmarked, rifling in a clever Joao Mario cutback from a corner in the 16th minute.
DOUBLE BLOW
The hosts, however, were dealt a double blow a little later with Slimani, a constant threat up front, forced off with an injury before Brazilian Mauricio clattered into Marco Hoeger for a second booking and a red card in the 33rd minute.
Schalke made the extra man count seconds later when Nigerian Chinedu Obasi headed in his first Champions League goal with the ball dribbling over the line after keeper Rui Patricio had failed to hold on to it.
Sporting, who have never won in Germany, found themselves facing an uphill struggle in the second half and Huntelaar needed only six minutes after the restart to net his third goal of the campaign in as many games.
Hoewedes, making his first appearance in the competition after recovering from a hip injury in September, headed in Schalke's third goal on the hour as the hosts looked to be cruising to victory.
But far from giving up, Sporting battled on and Silva cut the deficit with a well-taken spot kick three minutes later, before heading his second goal at the far post for what would have been an unlikely draw before Choupo-Moting's late decider.
"We showed an amazing spirit of sacrifice," Silva said. "We deserved another result for all we did during the match. We thought we had done enough to get the draw."
(Reporting by Karolos Grohmann; editing by Toby Davis)
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