O'Neill this week agreed to take charge of Blackburn alongside his role as Northern Ireland manager until the end of the season.
As well as trying to steer Northern Ireland to the World Cup via the play-offs - they face Italy in the semi-finals - O'Neill will also bid to keep Blackburn in the second tier.
He inherited a side third-bottom of the table, having won just one of their previous 10 league matches and only two of their past 16, but victory lifted them out of the relegation zone and up to 19th.
Jorgensen put them ahead on 21 minutes and restored the lead after Koki Saito's equaliser, before Ryoya Morishita's goal early in the second half sealed the victory.
Millwall boosted their promotion push with a 2-1 win at bottom of the table Sheffield Wednesday.
Having not scored a goal since Boxing Day, Wednesday took a shock lead when Jamal Lowe punished an error from Millwall goalkeeper Max Crocombe in the 60th minute.
Millwall hit back with two goals in two minutes as Cole McGhee prodded Tommy Watson's shot into his own net, before Macaulay Langstaff converted Femi Azeez's cross.
The Lions are up to third place, three points behind second-placed Coventry, who face leaders Middlesbrough on Monday.
Milutin Osmajic came off the bench to rescue Preston in a 2-2 draw with fellow play-off hopefuls Watford at Deepdale.
It was the first match in charge for new Watford boss Edward Still, brother of former Southampton manager Will Still.
Derby celebrated a home win for only the second time this year as they beat Swansea 2-0 at Pride Park to move into the play-off places.
Andre Brooks scored a 90th-minute winner as Sheffield United kept their play-off hopes alive with a 1-0 win at Portsmouth.