The development, which was widely expected, was significant in that it was announced just hours before the UK was due to formally trigger divorce proceedings from the EU.
The LSE had previously warned the tie-up was all but dead in the water because it would not meet a requirement that it sell a 60% stake in a bond trading platform called MTS.
It described that regulatory demand as "disproportionate".
A deal would have created a trading powerhouse - headquartered in London - to rival the biggest US operators and it remained on track through last summer despite doubts raised by the UK's Brexit vote.
The European Commission ruled against it on competition grounds, saying it would have created a "de facto monopoly" in Europe.
Margrethe Vestager, the EU's competition commissioner, said: "The European economy depends on well-functioning financial markets.
"That is not just important for banks and other financial institutions. The whole economy benefits when businesses can raise money on competitive financial markets.
"The merger between Deutsche Boerse and the London Stock Exchange would have significantly reduced competition by creating a de facto monopoly in the crucial area of clearing of fixed income instruments.
"As the parties failed to offer the remedies required to address our competition concerns, the Commission has decided to prohibit the merger."
The LSE Group, which had already offered to sell off its French clearing business LCH SA to help satisfy Commission concerns, responded: "LSEG believes the proposed merger with Deutsche Boerse in combination with the LCH SA remedy would have preserved credible and robust competition in all markets.
"This was an opportunity to create a world-leading market infrastructure group anchored in Europe, which would have supported Europe's 23 million SMEs and the development of a deeper Capital Markets Union."
LSE said it was "confident in its prospects as a standalone business" and would move to enhance the value of its stock through a £200m share buyback.
Its shares were up to 3.8% up in the wake of that announcement - later settling 2.7% higher at the close.
The ruling marked the third failed attempt at a merger between the pair in 17 years and it could be seen as an opportunity for Intercontinental Exchange (NYSE: ICE - news) (ICE), the owner of the New York Stock Exchange, to renew its interest in LSE.
John Colley, a Professor of Practice at Warwick Business School, said: "Whilst the business is performing well at the moment there is very likely to be some fallout from Brexit.
"A weakened LSE may need to look west for a future partner and strategy.
"There is likely to be plenty of interest from that quarter where Chicago's ICE has grown rapidly in recent years through acquisition.
"Dollar strength against Sterling and low costs of borrowing suggest that ICE will come calling very quickly."
Deutsche Boerse chairman Joachim Faber described the ruling as a "setback for Europe, the Capital Markets Union and the bridge between continental Europe and Great Britain."