Everton had offered next to no attacking threat in a game they were second best in for large periods but Rooney slammed home from the spot with 14 minutes left after Dejan Lovren had bundled Dominic Calvert-Lewin over in the box, a decision furiously protested by the Liverpool defender.
Mohamed Salah had earlier given Jurgen Klopp's side a deserved lead to continue his sensational season.
The winger curled home a wonderful effort from 15 yards in the 42nd minute to take him above Harry Kane as the Premier League's outright top scorer this season.
The goal was no more than Liverpool deserved in a completely one-sided first half in which Jordan Henderson completed more passes than then entire Everton side combined.
But Salah missed a golden opportunity to put the game to bed with a back-post header shortly after the break and the Toffees took full advantage of that reprieve to maintain Sam Allardyce's unbeaten start to life at the club.
Klopp made the surprise decision to name Roberto Firmino and Philippe Coutinho on the substitutes' bench, but the Brazilian duo's absence was hardly felt in the early stages with Sadio Mane, James Milner and Salah all seeing shots deflected or blocked by a stretched Everton backline.
Allardyce's side soon found their defensive shape, however, and largely reduced the Reds to efforts from distance as the first half wore on.
Salah had been well shackled by Cuco Martina in a strangely subdued appearance, but he spectacularly got the better of the Toffees left-back as the interval approached.
The Egypt international showed superb strength to shrug off Martina before waltzing past the challenge of Idrissa Gueye and curling in a wonderful strike into Jordan Pickford's top right-hand corner for his 13th league goal of the season.
Klopp's side should then have had a second in first-half injury time, but Mane dragged his shot wide when a pass across goal would have presented any one of three of his team-mates with a simple tap-in.
Allardyce hauled off Tom Davies and Oumar Niasse for Morgan Schneiderlin and Aaron Lennon at the break as Everton attempted to claw their way back into game.
Normal service was resumed just a few minutes later, though, as Salah met Milner's teasing cross at the back post, only to head agonisingly wide of Pickford's far post.
Alex Oxlade-Chamberlain's whipped cross midway through the half was just inches away from being converted by Mane as Liverpool continued to look like the only side capable of scoring.
But Liverpool were made to pay for their profligacy when Lovren inexplicably pushed Calvert-Lewin over in the area, with referee Craig Pawson pointing to the spot despite the Croatia international's complaints.
And Rooney thrashed the resulting spot-kick past Simon Mignolet for his fifth goal in his last six Premier League starts against the Reds.
Coutinho and Firmino both came on in the second period, but neither were able to find a winner as Everton held on for a point that scarcely looked likely until Lovren's moment of madness, while Liverpool missed the chance to go above third-placed Chelsea, despite their unbeaten derby run reaching 15 games.
15 - Liverpool are unbeaten in their last 15 games in all comps vs Everton – equalling their longest-ever such run against their Merseyside rivals (set between March 1972 and April 1978). Streak. pic.twitter.com/2CHlx0TcpV — OptaJoe (@OptaJoe) December 10, 2017
Key Opta Stats:
- Everton have lost just one of their last six Premier League games (W3 D2), after losing six of the eight before that (W1 D1).
- The Toffees posted a 21 per cent possession figure in the game, their lowest-ever in a Premier League since 2003/04 (when Opta started recording possession).
- Mohamed Salah has been directly involved in 23 goals for Liverpool in all competitions this season (in 24 games), two more than any other player in the Premier League.
- Salah has scored 19 goals in 24 appearances for Liverpool this season (all competitions), as many as he netted for Roma last term in 41 games
- Wayne Rooney has been directly involved in five goals in his last three Premier League games (4 goals, one assist), one more than he managed in his previous 11 with Everton this season.
- Danny Ings appeared in the Premier League for the first time since May 15, 2016 for Liverpool against West Brom 574 days ago.