Sunoco shares ended the day more than 3 percent lower while shares of Energy Transfer Partners declined 7 percent.
Sunoco Logistics said it agreed to acquire Energy Transfer Partners in a deal valued at $19.93 billion on Monday.
"Pipelines are going to be winners under Trump," Jim Cramer said on "Squawk on the Street." "Energy Transfer's been trying to build that national network of natural gas. This is a very important deal and it's out of nowhere, and this group is finally going to break out."
Jay Hatfield, portfolio manager of Infracap's MLP ETF, said the uncertainty surrounding the Dakota Access Pipeline may be a factor, as well as Sunoco's company size relative to Energy Transfer.
"We believe that the initial negative stock price reaction for SXL/ETP is driven by the fact that SXL, the acquirer, is a much smaller company than ETP and the merger will result in a net implicit reduction in dividend yield for ETP holders," Hatfield said.
The two companies did not immediately respond to CNBC's request for comment on the stock move.