Construction work started around April last year, but he said there was no evidence that the question of whether an EIA or planning permission were needed had properly been considered.
When TfL was asked why permission had not been sought, it described the superhighway as "works of improvement" not requiring permission or an EIA, said Mr Lowe.
He asked the judge to rule that construction of the superhighway was a "development" as defined under the Town and Country Planning Act 1990 and not exempt from the need for permission, especially as it was likely to give rise to "significant adverse environmental effects".
Dismissing the LTDA case, the judge ruled the TfL did not err in law, "and was not irrational in reaching its conclusion that there was no significant adverse environmental effect from the proposals as a whole."
The judge also declared: "On the evidence before the court, planning permission is not required for phase one of the superhighway as a whole.
"That is not to say that it may not be required for certain minor works within the scheme, or that it may not be required for other cycle superhighways or for parts of them in the future.
"Each scheme will need to be judged on its own facts."
Howard Carter, general counsel at TfL, said: "The east-west cycle superhighway will make London's roads safer for all, particularly cyclists."
Leon Daniels, managing director of TfL Surface Transport, added: "The court agreed with us that planning permission was not required for the construction of the route to date, and dismissed all aspects of the LTDA's claim.
"Construction continues to progress well and we are working hard to manage areas of temporary congestion around the construction sites.
"This cycle superhighway will make London's roads safer for all and encourage a more efficient use of the road space."
The mayor's cycling commissioner Andrew Gilligan said: "Once again, the courts have in the clearest terms upheld our right to improve London for cycling.
"This is the third legal challenge to TfL-funded cycle schemes to have been dismissed in the last few months.
"It means we can now be confident of finishing the Embankment/ Upper Thames Street superhighway on schedule in April, finishing the whole superhighway in summer, and ending the temporary delays that have occurred as a result of the construction works."
British Cycling’s campaign manager, Martin Key, welcomed the ruling.
He said: “The ruling should give transport authorities the confidence that they have the powers to develop the type of segregated cycle tracks needed to get people cycling.
"This is not about an ‘us and them’ mentality; the vast majority of people who cycle also drive, and we look forward to working with taxi firms and other road user groups to make the roads more accommodating for all.”
When the legal challenge was first announced, many cyclists threatened on Twitter to withdraw their custom from black cabs, and some said they would use rival Uber instead.
