NYSE Euronext completed its acquisition of the American Stock Exchange on Wednesday, making it the third-largest U.S. options marketplace and one of the leading markets for trading exchange-traded funds, equities, closed-end funds and structured products.

The transaction is expected to produce annualized run-rate cost savings in excess of $100 million by the end of 2009 and be accretive to earnings, the firm says.

With the acquisition of the Amex, NYSE Euronext will now operate a dual market structure offering the choice of price-time priority on NYSE Arca and the Amex’s traditional market-maker model. It also adds the Amex’s 416 ETFs and 13 exchange-traded note listings, 420 listings of closed-end funds and structured products, and more than 500 Amex-listed companies.

In December, the equities trading platform will transition to NYSE Euronext technology and Amex systems will be retired. In addition, NYSE Euronext plans to relocate Amex’s options trading floor operations to the NYSE options trading floor during the first quarter of 2009 and to transfer the Amex-supported technology to NYSE Euronext-supported technology for electronic options trading.

“This combination is beneficial to our customers and shareholders, further improves our competitive position in U.S. options, ETFs and cash equities, and enables us to realize significant operational efficiencies and new business opportunities,” says Duncan Niederauer, NYSE Euronext CEO. “Amex customers will have more products and services available to them and the advantage of leading-edge technology.”