However, a new Olympic Record from Lasse Norman Hansen (bettering the one set by Bradley Wiggins at Beijing 2008) won the event.
Hansen now leads overall after victory in the pursuit was added to his win in the scratch race earlier in the evening.
Cavendish came into the race with a sixth place in the scratch race earlier in the evening, and did his overall ambitions for a medal a huge favour with his performance in the second event.
The Manxman went head-to-head with former trade teammate Fernando Gaviria (Colombia), but caught and passed the present pursuit world champion during the 4km race.
Cavendish is not normally associated with the pursuit, preferring the more explosive disciplines of the omnium.
Both riders had the early benchmark of Elia Viviani (Italy) to aim for as they completed 16 laps of the velodrome.
Cavendish went out fast and held the pace for the whole ride but his leading time only lasted for a short period before Hansen set the new record and won the second omnium event.
The riders face the elimination race to finish the track cycling session on Sunday August 14, with the final three events split across the two sessions on Monday.
More from the Olympics
Your guide to the omnium
Men’s omnium: 4000m individual pursuit
1. Lasse Norman Hansen (DEN) 4:14.982 [Olympic record]
2. Mark Cavendish (GBR) 4:16.878
3. Elia Viviani (ITA) 4:17.453
4. Roger Kluge (GER) 4:18.907
5. Thomas Boudat (FRA) 4:19.918
6. Dylan Kennett (NZL) 4:20.180
7. Tim Veldt (NED) 4:22.856
8. Bobby Lea (USA) 4:23.942
9. Gideoni Monteiro (BRA) 4:25.808
10. Fernando Gaviria (COL) 4:26.649
11. Glenn O’Shea (AUS) 4:28.350
12. Sanghoon Park (KOR) 4:29.079
13. Chun Wing Leung (HKG) 4:29.162
14. Ignacio Prado (MEX) 4:29.396
15. Artyom Zakharov (KAZ) 4:32.503
16. Jasper De Buyst (BEL) 4:36.246
17. Gael Suter (SUI) 4:36.674
18. Kazushige Kuboki (JPN) 4:39.889
Overall top ten after two rounds
1. Lasse Norman Hansen (DEN) 80
2. Roger Kluge (GER) 72
3. Mark Cavendish (GBR) 68
4. Thomas Boudat (FRA) 68
5. Elia Viviani (ITA) 64
6. Glenn O’Shea (AUS) 54
7. Fernando Gaviria (COL) 54
8. Dylan Kennett (NZL) 52
9. Tim Veldt (NED) 48
10. Park Sanghoon (KOR) 42
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