With a 161 majority, victory should never have been in doubt. Left-wing rebels and disgruntled ex-ministers would oppose any fees rise. But normally loyal backbenchers opposed variable fees on principle (as did Labour's 2001 manifesto), knowing that a higher fixed fee could raise similar funds.
Nevertheless, Education Secretary Charles Clarke and higher education minister Alan Johnson emerge strengthened. By adding grants, bursaries and the fees regulator - and abolishing up-front fees - they made more palatable a policy decided before their appointments to the department.
Two factors helped win over Labour doubters. The first was the shrewd drip-feeding of relatively minor concessions. The second was that Norwich Labour MP Ian Gibson's key amendment seemed to have been drafted with Conservative help.
Ministers are also winning the public debate. A majority now accepts that graduates should pay towards university expansion. Yet fears remain that newer universities will lose out. And more money is needed to help working-class youngsters get the right A-levels.
Moreover, the economic argument for expansion is not wholly won. New research this week talked of a graduate "glut". Industry may believe the economy needs more graduates, but many of the public remain unconvinced.
The Bill faces a rough ride in the Lords. But, if senior Conservative peers back top-up fees - as Robert Jackson, the former higher education minister, did on Wednesday - that will also highlight opposition policy problems.
The party's existing commitment to scrap fees horrifies vice-chancellors.
Producing credible plans by the summer will be a tough balancing act. There will be wider implications. With other controversial votes, top-up fees have swelled the ranks of Labour rebels, who will be more powerful if the party has a reduced majority after the next election.
Prime Minister Tony Blair will still press ahead with more reform involving co-payment - where consumers share the cost of improved public services.
Childcare and school transport are next. Mr Blair must lay the groundwork properly next time.