Rominger, a novice at indoor track racing, covered 53.832km, 792m more than the Spanish cyclist.
It was the 33-year-old's first attempt at the mark, carried out behind closed doors and only regarded as a warm-up before a serious attempt next month.
It was also the third time in sixth months that the record had been beaten at the same track. Indurain, the four-times Tour de France winner who destroyed Rominger's dream of winning the race this year, had set a new mark of 53.040km at the same track on 2 September, beating the Scot Graeme Obree's 52.713km recorded in April.
Obree's effort in turn had eclipsed the Englishman Chris Boardman's 52.270km, which came in Bordeaux in July last year.
Rominger is currently ranked the world No 1 after winning the Tour of Spain this season for the third year in a row.
Rominger, who only started training for the attempt a week ago, was already five seconds ahead of Indurain's split after 5km and he passed 25km in 27min 49.79sec, almost half a minute quicker than the Spaniard.
He is expected to try to better his record at altitude in Mexico or Ecuador during the next few weeks, when he will use a specially designed bike.
Rominger used a normal track bike on Saturday, not a hi-tech machine as used by Indurain and Boardman. In contrast, Obree used a revolutionay home-made bike, later outlawed by cycling's ruling body.Reuse content